import multi-element compatible pair style edip as edip/multi
This commit is contained in:
Axel Kohlmeyer
26
examples/USER/misc/edip/Si.edip
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26
examples/USER/misc/edip/Si.edip
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# DATE: 2011-09-15 CONTRIBUTOR: Unknown CITATION: Justo, Bazant, Kaxiras, Bulatov and Yip, Phys Rev B, 58, 2539 (1998)
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# EDIP parameters for various elements and mixtures
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units
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# format of a single entry (one or more lines)
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#
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# element 1, element 2, element 3,
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# A B cutoffA cutoffC alpha beta eta
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# gamma lambda mu rho sigma Q0
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# u1 u2 u3 u4
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#
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# units for each parameters:
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# A , lambda are in eV
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# B, cutoffA, cutoffC, gamma, sigma are in Angstrom
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# alpha, beta, eta, mu, rho, Q0, u1-u4 are pure numbers
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# Here are the original parameters in metal units, for Silicon from:
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# J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip
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# Phys. Rev. B 58, 2539 (1998)
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#
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Si Si Si 7.9821730 1.5075463 3.1213820 2.5609104 3.1083847 0.0070975 0.2523244
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1.1247945 1.4533108 0.6966326 1.2085196 0.5774108 312.1341346
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-0.165799 32.557 0.286198 0.66
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38
examples/USER/misc/edip/SiC.edip
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38
examples/USER/misc/edip/SiC.edip
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# DATE: 2017-05-16 CONTRIBUTOR: Laurent Pizzagalli CITATION: G. Lucas, M. Bertolus, and L. Pizzagalli, J. Phys. : Condens. Matter 22, 035802 (2010)
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# element 1, element 2, element 3,
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# A B cutoffA cutoffC alpha beta eta
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# gamma lambda mu rho sigma Q0
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# u1 u2 u3 u4
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#
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Si Si Si 5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.589390
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1.135256 2.417497 0.629131 1.343679 0.298443 208.924548
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-0.165799 32.557 0.286198 0.66
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C C C 10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.275605
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1.084183 3.633621 0.594236 2.827634 0.536561 289.305617
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-0.165799 32.557 0.286198 0.66
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C Si Si 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497
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1.191567 3.025559 0.611684 2.061835 0.423863 249.115082
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-0.165799 32.557000 0.286198 0.660000
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Si C C 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497
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1.191567 3.025559 0.611684 2.061835 0.423863 249.115082
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-0.165799 32.557000 0.286198 0.660000
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Si Si C 5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.510944
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1.135256 2.721528 0.620407 1.343679 0.298443 229.019815
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-0.165799 32.557000 0.286198 0.660000
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Si C Si 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.510944
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1.191567 2.721528 0.620407 2.061835 0.423863 229.019815
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-0.165799 32.557000 0.286198 0.660000
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C C Si 10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.354051
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1.084183 3.329590 0.602960 2.827634 0.536561 269.210350
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-0.165799 32.557000 0.286198 0.660000
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C Si C 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.354051
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1.191567 3.329590 0.602960 2.061835 0.423863 269.210350
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-0.165799 32.557000 0.286198 0.660000
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138
examples/USER/misc/edip/data.SiC
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138
examples/USER/misc/edip/data.SiC
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Position data for Silicon-Carbon system
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128 atoms
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2 atom types
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-6.00 5.97232152 xlo xhi
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-6.00 5.97232152 ylo yhi
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-6.00 5.97232152 zlo zhi
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Atoms
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1 2 -2.9378454 -4.4592615 -4.8109196
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2 2 5.6222143 -2.7335026 -1.7157569
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3 2 -2.6614623 -5.5431059 1.6353686
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4 2 -5.4326838 -4.6174577 5.9452279
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5 2 5.8679239 -0.1120535 -3.5839373
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6 2 -3.7174621 -0.6623311 -0.3714789
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7 2 -5.0724728 -2.5671623 4.4103461
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8 2 -3.3951436 0.9341126 4.9310702
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9 2 -5.4347593 1.9523767 -5.6180938
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10 2 -4.5884719 2.2904528 -1.0597739
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11 2 -5.9058662 0.6212406 2.0127574
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12 2 -4.7680660 0.1965740 4.3267764
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13 2 -5.4228882 5.2569673 -4.5162920
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14 2 -5.2683965 -5.9193658 -2.8648668
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15 2 -2.8610884 1.0484664 2.0299077
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16 2 -4.0711084 5.3133026 3.8009514
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17 2 -0.1947147 -4.1677696 -5.6950931
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18 2 -2.9892710 -3.1647368 -1.6173910
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19 2 -0.9129311 -4.3819066 -0.1601859
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20 2 -2.4513693 -5.2466501 4.8882912
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21 2 -2.8879952 -0.1633446 -3.3401150
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22 1 -4.6738762 -1.3807254 -2.2946777
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23 2 -0.6973948 -1.4885343 0.6005156
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24 1 -2.7392164 -2.4774843 0.2387186
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25 2 -2.6551254 -2.7229952 2.6350264
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26 1 -3.4644263 -4.6028144 3.3817786
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27 2 0.7227614 -2.0709446 2.9214737
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28 1 -2.1000577 -3.2131296 5.7273437
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29 2 -3.1057649 2.3204819 -2.2725622
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30 1 -2.2298751 0.7168389 -1.3107201
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31 2 -1.8698261 1.4006751 0.7265108
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32 1 -4.1103409 -0.7093340 1.9341753
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33 2 -0.3505581 3.2707182 -0.2880656
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34 1 -3.4045407 -1.4383961 4.3903527
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35 2 -3.0940529 1.4132478 -5.3635505
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36 1 -4.4560663 1.2072875 -3.7310176
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37 2 -2.6061002 4.6373499 -4.6903941
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38 1 -3.3477444 4.6768137 -2.6284678
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39 2 0.8121697 4.8602418 -4.6710946
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40 1 -2.5756922 3.3740738 -0.2136350
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41 2 -0.3867976 5.8745611 -2.1119905
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42 1 -1.6766249 1.3374292 3.8741477
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43 2 -0.8770613 3.3735941 4.3846975
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44 1 -1.8609254 3.3158245 -5.9786556
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45 1 -5.2732321 -4.6073253 -0.9581754
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46 1 -2.7888697 -5.6910152 -0.7922023
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47 1 -2.4717165 4.5801880 2.5083210
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48 1 -3.8819950 5.8456589 -5.7563384
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49 2 2.2314782 -2.7729214 -5.2356862
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50 2 0.2981976 -3.1385279 -3.1608167
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51 2 2.8810785 -3.4658695 -0.5823196
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52 2 0.2509625 -5.7595229 2.7389761
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53 2 -0.2934120 -0.8029431 -3.3698507
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54 1 -1.0075690 -2.0481922 -1.9419298
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55 2 2.0729069 1.4922441 -2.3898096
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56 1 1.1110944 -3.2004208 0.9491078
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57 2 1.6774298 -0.7901860 2.5158773
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58 1 -0.8342297 -4.3342518 2.0971458
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59 2 3.2747406 -1.3107897 4.7884706
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60 1 1.7126246 -3.3691471 4.5581012
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61 2 0.4770605 1.7769008 -5.3339915
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62 1 0.2944391 0.5892781 -2.2030106
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63 2 2.2039275 3.1557557 -2.0276796
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64 1 -0.0404494 0.4767818 1.0396418
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65 2 1.1395867 2.3763443 2.3481007
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66 1 -0.9738374 -1.6325161 3.7538567
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67 2 -0.3291998 0.2996990 5.2770809
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68 1 -1.6185604 -0.3964274 -5.1771220
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69 2 2.5999949 -5.1977715 5.8230717
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70 1 -1.6270675 2.3210900 -3.6299941
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71 2 3.6532700 4.9282597 -5.4319276
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72 1 0.0788934 4.0241037 -2.5011530
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73 2 2.8556507 2.6168653 2.1125546
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74 1 0.9738989 2.6255364 4.3412121
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75 2 3.7452938 3.4521356 4.5946426
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76 1 2.0805182 4.7039015 5.3280260
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77 1 -1.0324174 -5.8155041 -4.3265820
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78 1 0.7622442 -4.3631629 -1.3156572
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79 1 0.3263684 3.9937357 1.6172321
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80 1 -0.4350105 -5.7997058 4.5959134
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81 2 3.9161132 -4.6052788 -3.3191717
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82 2 1.9240657 5.7345079 -1.9754251
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83 2 -5.9794488 -4.2369359 1.8646522
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84 2 4.3339975 -4.4845227 5.3737440
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85 2 2.2755456 -0.6327737 -5.7931837
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86 1 1.8728190 -1.5504906 -3.4560010
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87 2 3.4558100 -1.1054068 -1.8333071
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88 1 4.3788172 -1.9466494 -0.3284637
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89 2 2.5999235 -3.7548996 2.5740569
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90 1 3.9983910 -4.4856603 1.1968663
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91 2 -5.7295580 -2.1475672 -5.9963645
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92 1 4.2664051 -2.6988975 -5.8005478
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93 2 4.5254685 2.2906832 -3.4765798
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94 1 2.3603088 1.3416442 -4.4173836
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95 2 4.7767057 1.4061217 -0.7524620
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96 1 1.8072666 -0.7835973 -0.4581995
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97 2 4.4745018 0.3736224 2.1068274
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98 1 3.6081170 -1.7315713 2.4019053
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99 2 4.6281423 -0.2865409 4.4756524
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100 1 1.7975239 0.2893530 4.2330830
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101 2 5.8341452 4.4986472 -5.9664541
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102 1 3.2401308 4.1655227 -3.5070029
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103 2 4.8720339 4.8709982 -2.3364366
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104 1 3.5526476 1.2262752 0.6926826
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105 2 -5.8173342 4.5420479 1.5578881
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106 1 3.9683224 1.5441137 3.8284375
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||||
107 2 -5.5349308 1.9067049 3.7504113
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||||
108 1 4.4728615 2.6415574 -5.5952809
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||||
109 1 1.7000950 -4.8115440 -4.1953920
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||||
110 1 1.7221527 4.1878404 -0.3712681
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111 1 3.9218156 4.5935583 1.3263407
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112 1 3.1310195 -5.8922481 3.6001155
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113 1 4.7558719 -2.2877771 -3.4742052
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114 1 -5.5050300 -2.7027381 0.8748867
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115 1 5.8418594 -4.6064370 3.8714113
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116 1 -4.7516868 -3.1691984 -4.4099768
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117 1 3.9404971 0.7188702 -2.2898786
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118 1 -5.6869740 0.2042380 -0.1916738
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119 1 5.8949589 -1.2422560 3.1201292
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120 1 5.9675804 -0.0712572 5.8964022
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121 1 -5.6208517 3.3600036 -2.9493510
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122 1 5.2065263 3.4517912 -0.3800894
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123 1 -4.6994522 2.5489583 1.8297431
|
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124 1 -4.0758407 3.0726196 5.0647973
|
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125 1 4.1587591 -5.0896820 -1.1443498
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126 1 -4.6963753 -5.7429833 1.1357818
|
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127 1 5.5994192 4.6887008 3.5948264
|
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128 1 5.0988369 -5.3774409 -4.9051267
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72
examples/USER/misc/edip/in.edip-Si
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72
examples/USER/misc/edip/in.edip-Si
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@ -0,0 +1,72 @@
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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# temperature
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variable t equal 1800.0
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# coordination number cutoff
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variable r equal 2.835
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# minimization parameters
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|
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variable etol equal 1.0e-5
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variable ftol equal 1.0e-5
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variable maxiter equal 100
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variable maxeval equal 100
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variable dmax equal 1.0e-1
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|
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# diamond unit cell
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|
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variable a equal 5.431
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lattice custom $a &
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a1 1.0 0.0 0.0 &
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a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
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region myreg block 0 4 &
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0 4 &
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0 4
|
||||
create_box 1 myreg
|
||||
create_atoms 1 region myreg
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
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||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
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delete_atoms group del
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|
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pair_style edip
|
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pair_coeff * * Si.edip Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
|
||||
72
examples/USER/misc/edip/in.edip-Si-multi
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72
examples/USER/misc/edip/in.edip-Si-multi
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@ -0,0 +1,72 @@
|
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|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
create_box 1 myreg
|
||||
create_atoms 1 region myreg
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * Si.edip Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
|
||||
33
examples/USER/misc/edip/in.edip-SiC
Normal file
33
examples/USER/misc/edip/in.edip-SiC
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@ -0,0 +1,33 @@
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.SiC
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * SiC.edip Si C
|
||||
|
||||
mass 1 28.085
|
||||
mass 2 12.001
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 1
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
167
examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1
Normal file
167
examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1
Normal file
@ -0,0 +1,167 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * Si.edip Si
|
||||
Reading potential file Si.edip with DATE: 2011-09-15
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.12138
|
||||
ghost atom cutoff = 4.12138
|
||||
binsize = 2.06069, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip/multi, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.5039 -2372.6618 0 -2253.8359 12261.807
|
||||
10 952.62744 -2316.428 0 -2253.6283 723.08194
|
||||
20 549.13801 -2289.442 0 -2253.2413 -2444.5204
|
||||
30 1047.0106 -2321.1523 0 -2252.1305 9013.201
|
||||
40 663.46141 -2294.2083 0 -2250.4711 2942.5348
|
||||
50 504.74535 -2282.849 0 -2249.5748 -461.44909
|
||||
60 1019.2173 -2315.5639 0 -2248.3744 7706.4286
|
||||
70 844.51195 -2302.5251 0 -2246.8526 3116.8302
|
||||
80 814.90407 -2299.3372 0 -2245.6166 794.77455
|
||||
90 1269.5636 -2327.4775 0 -2243.7845 7729.3968
|
||||
100 977.61563 -2306.1118 0 -2241.6647 2969.9939
|
||||
110 843.08539 -2295.6547 0 -2240.0763 1393.4039
|
||||
120 1161.6968 -2314.6587 0 -2238.0766 7398.3492
|
||||
130 918.19451 -2296.4321 0 -2235.9022 2537.3997
|
||||
140 881.42548 -2292.2768 0 -2234.1709 1550.3339
|
||||
150 1231.1005 -2313.1054 0 -2231.9479 8112.7566
|
||||
160 967.01862 -2293.332 0 -2229.5836 3422.9627
|
||||
170 833.51248 -2282.7489 0 -2227.8015 43.991459
|
||||
180 1240.8488 -2307.3633 0 -2225.5632 6557.8651
|
||||
190 1126.4621 -2297.1922 0 -2222.9328 4289.0067
|
||||
200 947.59571 -2283.29 0 -2220.822 586.2811
|
||||
210 1228.153 -2299.4702 0 -2218.5071 5315.0425
|
||||
220 1215.4104 -2295.9408 0 -2215.8176 4870.3417
|
||||
230 1112.436 -2286.7552 0 -2213.4204 2527.1879
|
||||
240 1300.081 -2296.6013 0 -2210.8965 5738.3708
|
||||
250 1192.5738 -2286.8463 0 -2208.2286 4076.49
|
||||
260 1004.7055 -2272.1753 0 -2205.9424 359.37589
|
||||
270 1241.2018 -2285.3632 0 -2203.5399 4160.5763
|
||||
280 1360.1974 -2290.325 0 -2200.6572 5802.3902
|
||||
290 1151.9365 -2273.9467 0 -2198.008 1418.8887
|
||||
300 1174.3518 -2273.0089 0 -2195.5925 1998.229
|
||||
310 1329.2727 -2280.5049 0 -2192.8757 4721.7297
|
||||
320 1284.4414 -2274.7519 0 -2190.0781 2985.4674
|
||||
330 1328.3761 -2274.9545 0 -2187.3844 4543.2109
|
||||
340 1446.3847 -2279.8693 0 -2184.5198 6254.4059
|
||||
350 1366.2165 -2271.7475 0 -2181.6828 3637.8335
|
||||
360 1358.9609 -2268.5982 0 -2179.0118 3049.5798
|
||||
370 1552.208 -2278.4802 0 -2176.1545 6334.0058
|
||||
380 1562.5295 -2276.1793 0 -2173.1732 5787.5547
|
||||
390 1415.5498 -2263.7824 0 -2170.4655 3438.5766
|
||||
400 1323.1568 -2255.1641 0 -2167.938 2427.2294
|
||||
410 1260.7186 -2248.5373 0 -2165.4273 1208.6299
|
||||
420 1282.1118 -2247.3718 0 -2162.8516 462.65374
|
||||
430 1451.944 -2255.7551 0 -2160.0391 2037.8025
|
||||
440 1568.9415 -2260.417 0 -2156.9882 3531.1602
|
||||
450 1565.8262 -2257.2396 0 -2154.0162 2586.7886
|
||||
460 1677.7143 -2261.7214 0 -2151.122 4112.9756
|
||||
470 1762.9071 -2264.4244 0 -2148.2089 5053.2139
|
||||
480 1704.5898 -2257.8678 0 -2145.4967 4077.4626
|
||||
490 1731.2619 -2257.1048 0 -2142.9753 4710.5263
|
||||
500 1723.9777 -2254.161 0 -2140.5118 4760.7295
|
||||
Loop time of 0.679564 on 1 procs for 500 steps with 511 atoms
|
||||
|
||||
Performance: 63.570 ns/day, 0.378 hours/ns, 735.765 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.65181 | 0.65181 | 0.65181 | 0.0 | 95.92
|
||||
Neigh | 0.013857 | 0.013857 | 0.013857 | 0.0 | 2.04
|
||||
Comm | 0.0033884 | 0.0033884 | 0.0033884 | 0.0 | 0.50
|
||||
Output | 0.00070739 | 0.00070739 | 0.00070739 | 0.0 | 0.10
|
||||
Modify | 0.0083694 | 0.0083694 | 0.0083694 | 0.0 | 1.23
|
||||
Other | | 0.001432 | | | 0.21
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 845 ave 845 max 845 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: 7902 ave 7902 max 7902 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7902
|
||||
Ave neighs/atom = 15.4638
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
167
examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4
Normal file
167
examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4
Normal file
@ -0,0 +1,167 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * Si.edip Si
|
||||
Reading potential file Si.edip with DATE: 2011-09-15
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.12138
|
||||
ghost atom cutoff = 4.12138
|
||||
binsize = 2.06069, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip/multi, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.3816 -2372.6618 0 -2253.844 12260.967
|
||||
10 938.75954 -2315.5185 0 -2253.6329 558.21646
|
||||
20 534.27233 -2288.4721 0 -2253.2514 -2710.768
|
||||
30 1043.7796 -2320.9485 0 -2252.1398 8679.4381
|
||||
40 658.0916 -2293.8597 0 -2250.4765 2165.3742
|
||||
50 517.93009 -2283.7238 0 -2249.5805 -1124.9373
|
||||
60 1063.3594 -2318.4409 0 -2248.3414 7277.8526
|
||||
70 868.14006 -2304.0134 0 -2246.7832 2050.2848
|
||||
80 826.37805 -2300.0187 0 -2245.5416 91.099408
|
||||
90 1289.6772 -2328.7151 0 -2243.6961 8180.7423
|
||||
100 976.36208 -2305.9371 0 -2241.5727 3614.0499
|
||||
110 810.81713 -2293.4705 0 -2240.0193 1359.368
|
||||
120 1165.707 -2314.9026 0 -2238.056 7336.45
|
||||
130 929.81245 -2297.139 0 -2235.8432 2793.8451
|
||||
140 804.47874 -2287.2074 0 -2234.174 704.92455
|
||||
150 1182.4141 -2310.0266 0 -2232.0787 7822.2337
|
||||
160 979.92391 -2294.2969 0 -2229.6977 3206.7458
|
||||
170 830.14748 -2282.6079 0 -2227.8824 -296.87377
|
||||
180 1271.1133 -2309.4274 0 -2225.6322 7199.614
|
||||
190 1209.6006 -2302.6407 0 -2222.9006 5528.3784
|
||||
200 954.67693 -2283.6621 0 -2220.7273 47.02795
|
||||
210 1260.814 -2301.5582 0 -2218.442 4829.788
|
||||
220 1274.9954 -2299.7285 0 -2215.6774 5518.0597
|
||||
230 1048.0074 -2282.398 0 -2213.3106 1754.4144
|
||||
240 1261.7072 -2294.1108 0 -2210.9356 5233.2712
|
||||
250 1272.6178 -2292.0793 0 -2208.1849 4795.9325
|
||||
260 989.14205 -2271.0278 0 -2205.8209 -820.1828
|
||||
270 1212.0445 -2283.4212 0 -2203.52 3395.8634
|
||||
280 1391.9572 -2292.3809 0 -2200.6194 6666.2451
|
||||
290 1093.1204 -2270.0421 0 -2197.9807 206.94523
|
||||
300 1159.4831 -2272.102 0 -2195.6657 778.53806
|
||||
310 1407.3528 -2285.6228 0 -2192.8463 5223.048
|
||||
320 1236.7163 -2271.5389 0 -2190.0113 1865.3943
|
||||
330 1258.8275 -2270.4611 0 -2187.4758 2333.3209
|
||||
340 1507.9519 -2283.9906 0 -2184.5824 6775.5456
|
||||
350 1366.5116 -2271.7287 0 -2181.6446 3432.115
|
||||
360 1305.2829 -2265.1092 0 -2179.0614 1498.4073
|
||||
370 1581.4335 -2280.4645 0 -2176.2122 6518.5597
|
||||
380 1589.5319 -2277.9428 0 -2173.1567 6334.6506
|
||||
390 1402.6781 -2262.9323 0 -2170.464 3278.3038
|
||||
400 1374.9587 -2258.5717 0 -2167.9307 3608.7284
|
||||
410 1295.7416 -2250.7752 0 -2165.3565 1877.5222
|
||||
420 1278.6727 -2247.1099 0 -2162.8164 1599.4181
|
||||
430 1508.1328 -2259.4245 0 -2160.0044 4300.2224
|
||||
440 1624.2957 -2263.9806 0 -2156.9026 4432.625
|
||||
450 1597.3356 -2259.263 0 -2153.9624 3370.3816
|
||||
460 1772.0922 -2267.9106 0 -2151.0895 5788.3214
|
||||
470 1806.4047 -2267.304 0 -2148.221 5950.1166
|
||||
480 1593.0406 -2250.7469 0 -2145.7294 2518.0576
|
||||
490 1660.9767 -2252.894 0 -2143.398 4282.1643
|
||||
500 1714.283 -2253.9295 0 -2140.9194 5740.0247
|
||||
Loop time of 0.205398 on 4 procs for 500 steps with 511 atoms
|
||||
|
||||
Performance: 210.324 ns/day, 0.114 hours/ns, 2434.304 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.16285 | 0.1688 | 0.17446 | 1.1 | 82.18
|
||||
Neigh | 0.0035172 | 0.0036234 | 0.0038214 | 0.2 | 1.76
|
||||
Comm | 0.018727 | 0.024851 | 0.030996 | 2.9 | 12.10
|
||||
Output | 0.0013061 | 0.0014012 | 0.0015635 | 0.3 | 0.68
|
||||
Modify | 0.0046582 | 0.0048603 | 0.0050988 | 0.2 | 2.37
|
||||
Other | | 0.001861 | | | 0.91
|
||||
|
||||
Nlocal: 127.75 ave 131 max 124 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 433.75 ave 441 max 426 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1979.5 ave 2040 max 1895 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 7918
|
||||
Ave neighs/atom = 15.4951
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
167
examples/USER/misc/edip/log.4May2017.g++.edip-Si.1
Normal file
167
examples/USER/misc/edip/log.4May2017.g++.edip-Si.1
Normal file
@ -0,0 +1,167 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style edip
|
||||
pair_coeff * * Si.edip Si
|
||||
Reading potential file Si.edip with DATE: 2011-09-15
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.12138
|
||||
ghost atom cutoff = 4.12138
|
||||
binsize = 2.06069, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.5039 -2372.6618 0 -2253.8359 12261.807
|
||||
10 952.62744 -2316.428 0 -2253.6283 723.08283
|
||||
20 549.138 -2289.442 0 -2253.2413 -2444.5194
|
||||
30 1047.0106 -2321.1522 0 -2252.1305 9013.2015
|
||||
40 663.46143 -2294.2083 0 -2250.4711 2942.5358
|
||||
50 504.74533 -2282.849 0 -2249.5748 -461.44817
|
||||
60 1019.2173 -2315.5639 0 -2248.3744 7706.429
|
||||
70 844.51197 -2302.5251 0 -2246.8526 3116.8313
|
||||
80 814.90406 -2299.3372 0 -2245.6165 794.77536
|
||||
90 1269.5635 -2327.4775 0 -2243.7845 7729.3971
|
||||
100 977.61566 -2306.1118 0 -2241.6647 2969.9952
|
||||
110 843.08538 -2295.6547 0 -2240.0763 1393.4046
|
||||
120 1161.6968 -2314.6587 0 -2238.0766 7398.3495
|
||||
130 918.19453 -2296.4321 0 -2235.9022 2537.4011
|
||||
140 881.42546 -2292.2768 0 -2234.1709 1550.3345
|
||||
150 1231.1005 -2313.1054 0 -2231.9479 8112.7568
|
||||
160 967.01865 -2293.332 0 -2229.5836 3422.964
|
||||
170 833.51246 -2282.7489 0 -2227.8015 43.99251
|
||||
180 1240.8487 -2307.3633 0 -2225.5632 6557.8652
|
||||
190 1126.4621 -2297.1922 0 -2222.9328 4289.0083
|
||||
200 947.5957 -2283.29 0 -2220.8219 586.28203
|
||||
210 1228.153 -2299.4702 0 -2218.5071 5315.0427
|
||||
220 1215.4104 -2295.9407 0 -2215.8176 4870.343
|
||||
230 1112.436 -2286.7552 0 -2213.4204 2527.1887
|
||||
240 1300.081 -2296.6013 0 -2210.8965 5738.3711
|
||||
250 1192.5739 -2286.8463 0 -2208.2286 4076.4913
|
||||
260 1004.7055 -2272.1753 0 -2205.9424 359.3769
|
||||
270 1241.2018 -2285.3632 0 -2203.5399 4160.5764
|
||||
280 1360.1974 -2290.325 0 -2200.6572 5802.3912
|
||||
290 1151.9366 -2273.9467 0 -2198.008 1418.8905
|
||||
300 1174.3518 -2273.0089 0 -2195.5925 1998.2297
|
||||
310 1329.2726 -2280.5049 0 -2192.8757 4721.7304
|
||||
320 1284.4414 -2274.7519 0 -2190.0781 2985.4687
|
||||
330 1328.3761 -2274.9545 0 -2187.3844 4543.2115
|
||||
340 1446.3847 -2279.8693 0 -2184.5198 6254.4071
|
||||
350 1366.2165 -2271.7475 0 -2181.6828 3637.8351
|
||||
360 1358.9609 -2268.5982 0 -2179.0118 3049.5811
|
||||
370 1552.2079 -2278.4802 0 -2176.1545 6334.0061
|
||||
380 1562.5295 -2276.1793 0 -2173.1731 5787.5565
|
||||
390 1415.5498 -2263.7823 0 -2170.4655 3438.5782
|
||||
400 1323.1568 -2255.1641 0 -2167.938 2427.2311
|
||||
410 1260.7186 -2248.5373 0 -2165.4273 1208.6316
|
||||
420 1282.1118 -2247.3718 0 -2162.8516 462.65508
|
||||
430 1451.9439 -2255.7551 0 -2160.0391 2037.8027
|
||||
440 1568.9415 -2260.417 0 -2156.9882 3531.1613
|
||||
450 1565.8261 -2257.2396 0 -2154.0161 2586.7896
|
||||
460 1677.7143 -2261.7214 0 -2151.122 4112.976
|
||||
470 1762.9071 -2264.4244 0 -2148.2089 5053.2148
|
||||
480 1704.5898 -2257.8678 0 -2145.4966 4077.4649
|
||||
490 1731.2619 -2257.1048 0 -2142.9753 4710.5276
|
||||
500 1723.9777 -2254.161 0 -2140.5118 4760.7316
|
||||
Loop time of 0.312472 on 1 procs for 500 steps with 511 atoms
|
||||
|
||||
Performance: 138.252 ns/day, 0.174 hours/ns, 1600.143 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.28525 | 0.28525 | 0.28525 | 0.0 | 91.29
|
||||
Neigh | 0.013753 | 0.013753 | 0.013753 | 0.0 | 4.40
|
||||
Comm | 0.0033333 | 0.0033333 | 0.0033333 | 0.0 | 1.07
|
||||
Output | 0.00071096 | 0.00071096 | 0.00071096 | 0.0 | 0.23
|
||||
Modify | 0.008044 | 0.008044 | 0.008044 | 0.0 | 2.57
|
||||
Other | | 0.001385 | | | 0.44
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 845 ave 845 max 845 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: 7902 ave 7902 max 7902 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7902
|
||||
Ave neighs/atom = 15.4638
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
167
examples/USER/misc/edip/log.4May2017.g++.edip-Si.4
Normal file
167
examples/USER/misc/edip/log.4May2017.g++.edip-Si.4
Normal file
@ -0,0 +1,167 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style edip
|
||||
pair_coeff * * Si.edip Si
|
||||
Reading potential file Si.edip with DATE: 2011-09-15
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.12138
|
||||
ghost atom cutoff = 4.12138
|
||||
binsize = 2.06069, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.3816 -2372.6618 0 -2253.8439 12260.967
|
||||
10 938.75954 -2315.5185 0 -2253.6329 558.21736
|
||||
20 534.27232 -2288.4721 0 -2253.2514 -2710.767
|
||||
30 1043.7796 -2320.9485 0 -2252.1398 8679.4385
|
||||
40 658.09162 -2293.8597 0 -2250.4765 2165.3752
|
||||
50 517.93008 -2283.7238 0 -2249.5805 -1124.9362
|
||||
60 1063.3594 -2318.4409 0 -2248.3414 7277.853
|
||||
70 868.14007 -2304.0133 0 -2246.7832 2050.2859
|
||||
80 826.37803 -2300.0187 0 -2245.5416 91.100098
|
||||
90 1289.6772 -2328.7151 0 -2243.6961 8180.7427
|
||||
100 976.36211 -2305.9371 0 -2241.5727 3614.0511
|
||||
110 810.81711 -2293.4705 0 -2240.0193 1359.3687
|
||||
120 1165.707 -2314.9026 0 -2238.056 7336.4505
|
||||
130 929.81248 -2297.139 0 -2235.8432 2793.8463
|
||||
140 804.47872 -2287.2074 0 -2234.174 704.92524
|
||||
150 1182.414 -2310.0266 0 -2232.0787 7822.2339
|
||||
160 979.92395 -2294.2969 0 -2229.6977 3206.7474
|
||||
170 830.14746 -2282.6079 0 -2227.8824 -296.87288
|
||||
180 1271.1133 -2309.4274 0 -2225.6322 7199.614
|
||||
190 1209.6006 -2302.6407 0 -2222.9006 5528.3799
|
||||
200 954.67692 -2283.6621 0 -2220.7272 47.02925
|
||||
210 1260.814 -2301.5582 0 -2218.442 4829.7879
|
||||
220 1274.9954 -2299.7285 0 -2215.6774 5518.0611
|
||||
230 1048.0074 -2282.398 0 -2213.3106 1754.4157
|
||||
240 1261.7071 -2294.1107 0 -2210.9356 5233.2714
|
||||
250 1272.6179 -2292.0793 0 -2208.1849 4795.934
|
||||
260 989.14207 -2271.0278 0 -2205.8209 -820.18098
|
||||
270 1212.0444 -2283.4212 0 -2203.52 3395.8631
|
||||
280 1391.9572 -2292.3809 0 -2200.6194 6666.2464
|
||||
290 1093.1205 -2270.0421 0 -2197.9807 206.94752
|
||||
300 1159.483 -2272.102 0 -2195.6657 778.53823
|
||||
310 1407.3528 -2285.6227 0 -2192.8463 5223.0487
|
||||
320 1236.7164 -2271.5389 0 -2190.0112 1865.3963
|
||||
330 1258.8275 -2270.4611 0 -2187.4758 2333.321
|
||||
340 1507.9519 -2283.9906 0 -2184.5824 6775.546
|
||||
350 1366.5116 -2271.7287 0 -2181.6446 3432.1175
|
||||
360 1305.2828 -2265.1091 0 -2179.0614 1498.4079
|
||||
370 1581.4334 -2280.4645 0 -2176.2122 6518.5598
|
||||
380 1589.5319 -2277.9428 0 -2173.1566 6334.6527
|
||||
390 1402.6782 -2262.9323 0 -2170.464 3278.3048
|
||||
400 1374.9587 -2258.5717 0 -2167.9307 3608.7293
|
||||
410 1295.7416 -2250.7752 0 -2165.3565 1877.5245
|
||||
420 1278.6727 -2247.1099 0 -2162.8164 1599.4189
|
||||
430 1508.1328 -2259.4245 0 -2160.0044 4300.2235
|
||||
440 1624.2957 -2263.9806 0 -2156.9026 4432.6267
|
||||
450 1597.3356 -2259.263 0 -2153.9623 3370.3829
|
||||
460 1772.0921 -2267.9105 0 -2151.0895 5788.3219
|
||||
470 1806.4047 -2267.304 0 -2148.221 5950.1188
|
||||
480 1593.0406 -2250.7469 0 -2145.7294 2518.0601
|
||||
490 1660.9766 -2252.894 0 -2143.398 4282.1654
|
||||
500 1714.2831 -2253.9295 0 -2140.9194 5740.0268
|
||||
Loop time of 0.109584 on 4 procs for 500 steps with 511 atoms
|
||||
|
||||
Performance: 394.220 ns/day, 0.061 hours/ns, 4562.726 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.074678 | 0.077817 | 0.084705 | 1.4 | 71.01
|
||||
Neigh | 0.0036662 | 0.0037943 | 0.0039661 | 0.2 | 3.46
|
||||
Comm | 0.013665 | 0.020312 | 0.023178 | 2.7 | 18.54
|
||||
Output | 0.0010247 | 0.0010931 | 0.0012922 | 0.3 | 1.00
|
||||
Modify | 0.0043213 | 0.0047521 | 0.0051889 | 0.6 | 4.34
|
||||
Other | | 0.001814 | | | 1.66
|
||||
|
||||
Nlocal: 127.75 ave 131 max 124 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 433.75 ave 441 max 426 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1979.5 ave 2040 max 1895 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 7918
|
||||
Ave neighs/atom = 15.4951
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
92
examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1
Normal file
92
examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.SiC
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * SiC.edip Si C
|
||||
Reading potential file SiC.edip with DATE: 2017-05-16
|
||||
|
||||
mass 1 28.085
|
||||
mass 2 12.001
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 1
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 1 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.94159
|
||||
ghost atom cutoff = 3.94159
|
||||
binsize = 1.97079, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip/multi, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.692 | 2.692 | 2.692 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -563.61621 0 -563.61621 -726147.34
|
||||
10 4224.3601 -633.24829 0 -563.90103 -312355.55
|
||||
20 4528.5661 -638.15183 0 -563.81071 -20091.291
|
||||
30 4817.3654 -642.92111 0 -563.83905 106625.5
|
||||
40 4619.4324 -639.6884 0 -563.85562 107180.42
|
||||
50 4783.0025 -642.26961 0 -563.75166 75134.335
|
||||
60 4525.145 -638.06177 0 -563.77681 71591.713
|
||||
70 4685.2578 -640.72377 0 -563.8104 63956.042
|
||||
80 4621.8393 -639.75912 0 -563.88682 18177.383
|
||||
90 4834.7702 -643.34582 0 -563.97805 15282.823
|
||||
100 4424.0589 -636.60208 0 -563.97656 47963.501
|
||||
Loop time of 0.0552888 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 156.270 ns/day, 0.154 hours/ns, 1808.685 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.051872 | 0.051872 | 0.051872 | 0.0 | 93.82
|
||||
Neigh | 0.0023525 | 0.0023525 | 0.0023525 | 0.0 | 4.25
|
||||
Comm | 0.0004518 | 0.0004518 | 0.0004518 | 0.0 | 0.82
|
||||
Output | 0.00014806 | 0.00014806 | 0.00014806 | 0.0 | 0.27
|
||||
Modify | 0.00024796 | 0.00024796 | 0.00024796 | 0.0 | 0.45
|
||||
Other | | 0.0002165 | | | 0.39
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 473 ave 473 max 473 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: 2376 ave 2376 max 2376 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2376
|
||||
Ave neighs/atom = 18.5625
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
92
examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4
Normal file
92
examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.SiC
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * SiC.edip Si C
|
||||
Reading potential file SiC.edip with DATE: 2017-05-16
|
||||
|
||||
mass 1 28.085
|
||||
mass 2 12.001
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 1
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 1 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.94159
|
||||
ghost atom cutoff = 3.94159
|
||||
binsize = 1.97079, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip/multi, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.686 | 2.686 | 2.686 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -563.61621 0 -563.61621 -726147.34
|
||||
10 4224.3601 -633.24829 0 -563.90103 -312355.55
|
||||
20 4528.5661 -638.15183 0 -563.81071 -20091.291
|
||||
30 4817.3654 -642.92111 0 -563.83905 106625.5
|
||||
40 4619.4324 -639.6884 0 -563.85562 107180.42
|
||||
50 4783.0025 -642.26961 0 -563.75166 75134.335
|
||||
60 4525.145 -638.06177 0 -563.77681 71591.713
|
||||
70 4685.2578 -640.72377 0 -563.8104 63956.042
|
||||
80 4621.8393 -639.75912 0 -563.88682 18177.383
|
||||
90 4834.7702 -643.34582 0 -563.97805 15282.823
|
||||
100 4424.0589 -636.60208 0 -563.97656 47963.501
|
||||
Loop time of 0.020755 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 416.285 ns/day, 0.058 hours/ns, 4818.118 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.011816 | 0.013825 | 0.016871 | 1.6 | 66.61
|
||||
Neigh | 0.00061321 | 0.00066817 | 0.00074816 | 0.0 | 3.22
|
||||
Comm | 0.0023363 | 0.0054012 | 0.0075014 | 2.7 | 26.02
|
||||
Output | 0.00020909 | 0.00022268 | 0.00025558 | 0.0 | 1.07
|
||||
Modify | 8.3208e-05 | 9.346e-05 | 0.00010395 | 0.0 | 0.45
|
||||
Other | | 0.0005446 | | | 2.62
|
||||
|
||||
Nlocal: 32 ave 36 max 25 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 262.75 ave 273 max 255 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 594 ave 687 max 453 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 2376
|
||||
Ave neighs/atom = 18.5625
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
Reference in New Issue
Block a user