mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12439 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
1b19868c97
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@ -89,6 +89,7 @@ peptide: dynamics of a small solvated peptide chain (5-mer)
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peri: Peridynamic model of cylinder impacted by indenter
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peri: Peridynamic model of cylinder impacted by indenter
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pour: pouring of granular particles into a 3d box, then chute flow
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pour: pouring of granular particles into a 3d box, then chute flow
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prd: parallel replica dynamics of vacancy diffusion in bulk Si
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prd: parallel replica dynamics of vacancy diffusion in bulk Si
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qeq: use of the QEQ pacakge for charge equilibration
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reax: RDX and TATB models using the ReaxFF
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reax: RDX and TATB models using the ReaxFF
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rigid: rigid bodies modeled as independent or coupled
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rigid: rigid bodies modeled as independent or coupled
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shear: sideways shear applied to 2d solid, with and without a void
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shear: sideways shear applied to 2d solid, with and without a void
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@ -0,0 +1,122 @@
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# CHO example
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105 atoms
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3 atom types
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0 25.000 xlo xhi
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0 25.000 ylo yhi
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0 25.000 zlo zhi
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Masses
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1 1.0080
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2 12.0107
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3 15.9994
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Atoms
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1 2 0.0 10.67229 14.36836 12.47166
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2 1 0.0 11.02446 14.91550 13.35233
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3 1 0.0 11.02446 14.91549 11.59096
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4 1 0.0 9.57932 14.41980 12.47166
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5 2 0.0 11.17534 12.87608 12.47165
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6 1 0.0 10.79792 12.33546 13.34037
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7 1 0.0 10.79790 12.33545 11.60294
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8 2 0.0 12.75013 12.93134 12.47163
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9 1 0.0 13.13241 13.47175 11.60486
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10 1 0.0 13.13241 13.47210 13.33818
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11 2 0.0 13.22294 11.42815 12.47199
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12 1 0.0 12.83858 10.89166 11.60377
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13 1 0.0 12.83959 10.89255 13.34119
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14 2 0.0 14.79762 11.45137 12.47107
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15 1 0.0 15.21044 10.43808 12.47354
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16 1 0.0 15.19550 11.96345 11.58877
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17 1 0.0 15.19648 11.96815 13.35018
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18 2 0.0 0.24250 0.91354 1.10383
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19 1 0.0 0.97225 1.67509 1.39797
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20 1 0.0 24.87363 1.18825 0.11010
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21 1 0.0 24.39847 0.98637 1.79630
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22 2 0.0 0.86944 24.46895 1.11508
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23 1 0.0 1.21047 24.19771 2.11484
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24 1 0.0 0.12679 23.71752 0.84453
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25 2 0.0 2.06454 24.48829 0.08825
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26 1 0.0 1.72846 24.75977 24.08683
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27 1 0.0 2.80951 0.23920 0.35408
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28 2 0.0 2.67036 23.03401 0.12171
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29 1 0.0 1.92204 22.28680 24.85503
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30 1 0.0 3.00638 22.76782 1.12450
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31 2 0.0 3.87027 23.02208 24.10132
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32 1 0.0 4.35176 22.04072 24.06515
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33 1 0.0 3.54082 23.26189 23.08511
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34 1 0.0 4.63935 23.75310 24.37121
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35 2 0.0 1.37929 14.62909 17.52744
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36 1 0.0 1.08393 15.52196 18.08818
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37 1 0.0 2.47385 14.59977 17.52258
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38 1 0.0 1.05260 14.77122 16.49293
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39 2 0.0 0.76275 13.31937 18.14786
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40 1 0.0 24.67295 13.35030 18.12450
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41 1 0.0 1.04396 12.44064 17.56651
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42 2 0.0 1.30113 13.22425 19.62581
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43 1 0.0 2.39107 13.19385 19.65447
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44 1 0.0 1.02336 14.10169 20.21106
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45 2 0.0 0.66878 11.90830 20.21883
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46 1 0.0 0.94960 11.03396 19.63080
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47 1 0.0 24.57945 11.94426 20.18968
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48 2 0.0 1.19125 11.78568 21.69954
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49 1 0.0 0.79365 10.89123 22.18875
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50 1 0.0 2.28374 11.72162 21.74071
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51 1 0.0 0.89616 12.64769 22.30679
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52 2 0.0 11.41750 7.16471 22.76002
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53 1 0.0 11.74866 7.28340 21.72336
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54 1 0.0 11.72154 8.06612 23.30055
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55 1 0.0 11.97469 6.32478 23.18558
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56 2 0.0 9.86319 6.92474 22.85179
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57 1 0.0 9.57626 6.01094 22.33031
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58 1 0.0 9.54930 6.78307 23.88660
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59 2 0.0 9.17390 8.18942 22.21244
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60 1 0.0 9.45849 9.10599 22.73021
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61 1 0.0 9.48557 8.33580 21.17777
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62 2 0.0 7.62459 7.92132 22.31840
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63 1 0.0 7.31756 7.77569 23.35472
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64 1 0.0 7.34468 7.00469 21.79795
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65 2 0.0 6.90692 9.17258 21.68631
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66 1 0.0 5.81845 9.06496 21.71809
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67 1 0.0 7.15914 10.09632 22.21721
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68 1 0.0 7.18992 9.31630 20.63835
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69 2 0.0 4.69047 14.13340 23.48572
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70 1 0.0 4.95366 15.17281 23.26391
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71 1 0.0 5.39163 13.78010 24.24888
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72 1 0.0 4.87514 13.55000 22.57874
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73 2 0.0 3.19477 13.99798 23.95930
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74 1 0.0 2.50599 14.33002 23.18163
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75 1 0.0 2.93803 12.95591 24.15345
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76 2 0.0 3.05322 14.87431 0.26136
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77 1 0.0 3.74058 14.54651 1.04202
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78 1 0.0 3.30993 15.91730 0.07257
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79 2 0.0 1.55058 14.71961 0.71013
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80 1 0.0 1.29864 13.67531 0.89801
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81 1 0.0 0.86725 15.05003 24.92701
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82 2 0.0 1.37850 15.58633 2.01380
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83 1 0.0 0.35341 15.53527 2.39297
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84 1 0.0 2.04062 15.24695 2.81709
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85 1 0.0 1.60704 16.64178 1.83261
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86 3 0.0 8.51658 13.05007 22.43728
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87 3 0.0 9.43965 13.72051 21.88842
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88 3 0.0 18.16518 4.73455 8.81928
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89 3 0.0 18.65469 4.57291 7.66370
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90 3 0.0 6.43553 20.34119 24.80049
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91 3 0.0 6.44898 20.31621 23.53493
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92 3 0.0 21.90539 11.54301 19.82384
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93 3 0.0 20.76137 11.61918 20.36007
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94 3 0.0 3.42232 11.07545 5.77130
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95 3 0.0 3.88671 10.95299 4.60048
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96 3 0.0 11.93988 4.94134 20.86058
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97 3 0.0 12.98804 5.47798 20.39555
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98 3 0.0 14.08646 9.50799 20.80806
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99 3 0.0 14.09449 10.68237 20.33642
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100 3 0.0 3.45246 19.93144 16.38965
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101 3 0.0 2.86282 19.60263 15.31936
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102 3 0.0 12.85008 21.95287 13.63796
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103 3 0.0 12.06593 21.16486 14.24238
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104 3 0.0 24.47055 7.42219 14.24997
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105 3 0.0 24.43181 7.37102 12.98624
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,123 @@
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Reactive MD-force field c/h/o combustion force field: Chenoweth, K.; van Duin, A.C.T.; Goddard, W.A. J. Phys. Chem. A 2008, 112, 1040-1053.
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39 ! Number of general parameters
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50.0000 !p(boc1)
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9.5469 !p(boc2)
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26.5405 !p(coa2)
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1.5105 !p(trip4)
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6.6630 !p(trip3)
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70.0000 !kc2
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1.0588 !p(ovun6)
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4.6000 !p(trip2)
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12.1176 !p(ovun7)
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13.3056 !p(ovun8)
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-70.1292 !p(trip1)
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0.0000 !Lower Taper-radius (swa)
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10.0000 !Upper Taper-radius (swb)
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0.0000 !not used
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33.8667 !p(val7)
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6.0891 !p(lp1)
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1.0563 !p(val9)
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2.0384 !p(val10)
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6.1431 !not used
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6.9290 !p(pen2)
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0.3989 !p(pen3)
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3.9954 !p(pen4)
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0.0000 !not used
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5.7796 !p(tor2)
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10.0000 !p(tor3)
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1.9487 !p(tor4)
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0.0000 !not used
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2.1645 !p(cot2)
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1.5591 !p(vdW1)
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0.1000 !Cutoff for bond order*100 (cutoff)
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2.1365 !p(coa4)
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0.6991 !p(ovun4)
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50.0000 !p(ovun3)
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1.8512 !p(val8)
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0.0000 !not used
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0.0000 !not used
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0.0000 !not used
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0.0000 !not used
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2.6962 !p(coa3)
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3 ! Nr of atoms; atomID;ro(sigma); Val;atom mass;Rvdw;Dij;gamma;ro(pi);Val(e)
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alfa;gamma(w);Val(angle);p(ovun5);n.u.;chiEEM;etaEEM;n.u.
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ro(pipi);p(lp2);Heat increment;p(boc4);p(boc3);p(boc5),n.u.;n.u.
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p(ovun2);p(val3);n.u.;Val(boc);p(val5);n.u.;n.u.;n.u.
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C 1.3825 4.0000 12.0000 1.9133 0.1853 0.9000 1.1359 4.0000
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9.7602 2.1346 4.0000 33.2433 79.5548 5.8678 7.0000 0.0000
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1.2104 0.0000 199.0303 8.6991 34.7289 13.3894 0.8563 0.0000
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-2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000
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H 0.7853 1.0000 1.0080 1.5904 0.0419 1.0206 -0.1000 1.0000
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9.3557 5.0518 1.0000 0.0000 121.1250 5.3200 7.4366 1.0000
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-0.1000 0.0000 62.4879 1.9771 3.3517 0.7571 1.0698 0.0000
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-15.7683 2.1488 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000
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O 1.2477 2.0000 15.9990 1.9236 0.0904 1.0503 1.0863 6.0000
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10.2127 7.7719 4.0000 36.9573 116.0768 8.5000 8.9989 2.0000
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0.9088 1.0003 60.8726 20.4140 3.3754 0.2702 0.9745 0.0000
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-3.6141 2.7025 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000
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6 ! Nr of bonds; at1;at2;De(sigma);De(pi);De(pipi);p(be1);p(bo5);13corr;n.u.;p(bo6),p(ovun1)
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p(be2);p(bo3);p(bo4);n.u.;p(bo1);p(bo2)
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1 1 156.5953 100.0397 80.0000 -0.8157 -0.4591 1.0000 37.7369 0.4235
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0.4527 -0.1000 9.2605 1.0000 -0.0750 6.8316 1.0000 0.0000
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1 2 170.2316 0.0000 0.0000 -0.5931 0.0000 1.0000 6.0000 0.7140
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5.2267 1.0000 0.0000 1.0000 -0.0500 6.8315 0.0000 0.0000
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2 2 156.0973 0.0000 0.0000 -0.1377 0.0000 1.0000 6.0000 0.8240
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2.9907 1.0000 0.0000 1.0000 -0.0593 4.8358 0.0000 0.0000
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1 3 160.4802 105.1693 23.3059 -0.3873 -0.1613 1.0000 10.8851 1.0000
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0.5341 -0.3174 7.0303 1.0000 -0.1463 5.2913 0.0000 0.0000
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3 3 60.1463 176.6202 51.1430 -0.2802 -0.1244 1.0000 29.6439 0.9114
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0.2441 -0.1239 7.6487 1.0000 -0.1302 6.2919 1.0000 0.0000
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2 3 180.4373 0.0000 0.0000 -0.8074 0.0000 1.0000 6.0000 0.5514
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1.2490 1.0000 0.0000 1.0000 -0.0657 5.0451 0.0000 0.0000
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3 ! Nr of off-diagonal terms. at1;at2;Dij;RvdW;alfa;ro(sigma);ro(pi);ro(pipi)
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1 2 0.1219 1.4000 9.8442 1.1203 -1.0000 -1.0000
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2 3 0.0344 1.6800 10.3247 0.9013 -1.0000 -1.0000
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1 3 0.1131 1.8523 9.8442 1.2775 1.1342 1.0621
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18 ! Nr of angles. at1;at2;at3;Thetao,o;p(val1);p(val2);p(coa1);p(val7);p(pen1);p(val4)
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1 1 1 67.2326 22.0695 1.6286 0.0000 1.7959 15.4141 1.8089
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1 1 2 65.2527 14.3185 6.2977 0.0000 0.5645 0.0000 1.1530
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2 1 2 70.0840 25.3540 3.4508 0.0000 0.0050 0.0000 3.0000
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1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400
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1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400
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2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400
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1 1 3 49.5561 7.3771 4.9568 0.0000 0.7533 15.9906 1.0010
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3 1 3 77.1171 39.8746 2.5403 -24.3902 1.7740 -42.9758 2.1240
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2 1 3 65.0000 14.2057 4.8649 0.0000 0.3504 0.0000 1.7185
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1 3 1 74.3994 44.7500 0.7982 0.0000 3.0000 0.0000 1.0528
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1 3 3 77.9854 36.6201 2.0201 0.0000 0.7434 67.0264 3.0000
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3 3 3 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783
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1 3 2 71.5018 21.7062 0.4735 0.0000 0.5186 0.0000 1.1793
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2 3 3 84.9468 23.3540 1.5057 0.0000 2.6374 0.0000 1.3023
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2 3 2 77.0645 10.4737 1.2895 0.0000 0.9924 0.0000 1.1043
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1 2 3 0.0000 25.0000 3.0000 0.0000 1.0000 0.0000 1.0400
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3 2 3 0.0000 0.0148 6.0000 0.0000 0.0000 0.0000 1.0400
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2 2 3 0.0000 9.7025 6.0000 0.0000 0.0000 0.0000 1.0400
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26 ! Nr of torsions. at1;at2;at3;at4;;V1;V2;V3;p(tor1);p(cot1);n.u;n.u.
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1 1 1 1 -0.2500 11.5822 0.1879 -4.7057 -2.2047 0.0000 0.0000
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1 1 1 2 -0.2500 31.2596 0.1709 -4.6391 -1.9002 0.0000 0.0000
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2 1 1 2 -0.1770 30.0252 0.4340 -5.0019 -2.0697 0.0000 0.0000
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1 1 1 3 -0.7098 22.2951 0.0060 -2.5000 -2.1688 0.0000 0.0000
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2 1 1 3 -0.3568 22.6472 0.6045 -4.0088 -1.0000 0.0000 0.0000
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3 1 1 3 -0.0528 6.8150 0.7498 -5.0913 -1.0000 0.0000 0.0000
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1 1 3 1 2.0007 25.5641 -0.0608 -2.6456 -1.1766 0.0000 0.0000
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1 1 3 2 -1.1953 42.1545 -1.0000 -8.0821 -1.0000 0.0000 0.0000
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2 1 3 1 -0.9284 34.3952 0.7285 -2.5440 -2.4641 0.0000 0.0000
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2 1 3 2 -2.5000 79.6980 1.0000 -3.5697 -2.7501 0.0000 0.0000
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1 1 3 3 -0.0179 5.0603 -0.1894 -2.5000 -2.0399 0.0000 0.0000
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2 1 3 3 -0.5583 80.0000 1.0000 -4.4000 -3.0000 0.0000 0.0000
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3 1 3 1 -2.5000 76.0427 -0.0141 -3.7586 -2.9000 0.0000 0.0000
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3 1 3 2 0.0345 78.9586 -0.6810 -4.1777 -3.0000 0.0000 0.0000
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3 1 3 3 -2.5000 66.3525 0.3986 -3.0293 -3.0000 0.0000 0.0000
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1 3 3 1 2.5000 -0.5332 1.0000 -3.5096 -2.9000 0.0000 0.0000
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1 3 3 2 -2.5000 3.3219 0.7180 -5.2021 -2.9330 0.0000 0.0000
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2 3 3 2 2.2500 -6.2288 1.0000 -2.6189 -1.0000 0.0000 0.0000
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1 3 3 3 0.0531 -17.3983 1.0000 -2.5000 -2.1584 0.0000 0.0000
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2 3 3 3 0.4723 -12.4144 -1.0000 -2.5000 -1.0000 0.0000 0.0000
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||||||
|
3 3 3 3 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000
|
||||||
|
0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
|
||||||
|
0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
|
||||||
|
0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
|
||||||
|
0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000
|
||||||
|
0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000
|
||||||
|
1 ! Nr of hydrogen bonds. at1;at2;at3;r(hb);p(hb1);p(hb2);p(hb3)
|
||||||
|
3 2 3 1.9682 -4.4628 1.7976 3.0000
|
||||||
|
|
@ -0,0 +1,39 @@
|
||||||
|
# This example demonstrates the use of various fix qeq variants with
|
||||||
|
# that defines and uses charges, in this case pair_style buck/coul/long
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style charge
|
||||||
|
|
||||||
|
read_data data.aC
|
||||||
|
|
||||||
|
pair_style buck/coul/long 12.0
|
||||||
|
pair_coeff 2 2 1388.77 .3623188 175.0
|
||||||
|
pair_coeff 1 2 18003 .2052124 133.5381
|
||||||
|
pair_coeff 1 1 0 .1 0
|
||||||
|
kspace_style ewald 1e-6
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
group type1 type 1
|
||||||
|
compute charge1 type1 property/atom q
|
||||||
|
compute q1 type1 reduce ave c_charge1
|
||||||
|
group type2 type 2
|
||||||
|
compute charge2 type2 property/atom q
|
||||||
|
compute q2 type2 reduce ave c_charge2
|
||||||
|
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
|
||||||
|
|
||||||
|
thermo_style custom step pe c_q1 c_q2 v_qtot
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
|
||||||
|
velocity all create 300.0 1281937
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
|
||||||
|
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
|
||||||
|
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
|
||||||
|
fix 2 all qeq/dynamic 1 10 1.0e-2 100 param.qeq2
|
||||||
|
|
||||||
|
run 10
|
||||||
|
|
@ -0,0 +1,46 @@
|
||||||
|
# This example demonstrates the use of various fix qeq variants with pair reax/c
|
||||||
|
# You can comment in/out various versions below
|
||||||
|
#
|
||||||
|
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
||||||
|
# used with pair_style reax/c, provided that the QEq parameters are the same.
|
||||||
|
#
|
||||||
|
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
||||||
|
# the QEq parameters are the same. These two styles can also be used with
|
||||||
|
# pair_style reax/c.
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style charge
|
||||||
|
|
||||||
|
read_data data.CHO
|
||||||
|
|
||||||
|
pair_style reax/c NULL checkqeq no
|
||||||
|
pair_coeff * * ffield.reax.cho H C O
|
||||||
|
|
||||||
|
neighbor 1 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
group type1 type 1
|
||||||
|
compute charge1 type1 property/atom q
|
||||||
|
compute q1 type1 reduce ave c_charge1
|
||||||
|
group type2 type 2
|
||||||
|
compute charge2 type2 property/atom q
|
||||||
|
compute q2 type2 reduce ave c_charge2
|
||||||
|
group type3 type 3
|
||||||
|
compute charge3 type3 property/atom q
|
||||||
|
compute q3 type3 reduce ave c_charge3
|
||||||
|
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
|
||||||
|
|
||||||
|
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
velocity all create 300.0 1281937
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
|
||||||
|
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
|
||||||
|
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
|
||||||
|
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
|
||||||
|
|
||||||
|
timestep 0.25
|
||||||
|
|
||||||
|
run 10
|
||||||
|
|
@ -0,0 +1,85 @@
|
||||||
|
LAMMPS (5 Sep 2014)
|
||||||
|
# This example demonstrates the use of various fix qeq variants with
|
||||||
|
# that defines and uses charges, in this case pair_style buck/coul/long
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style charge
|
||||||
|
|
||||||
|
read_data data.aC
|
||||||
|
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
1200 atoms
|
||||||
|
|
||||||
|
pair_style buck/coul/long 12.0
|
||||||
|
pair_coeff 2 2 1388.77 .3623188 175.0
|
||||||
|
pair_coeff 1 2 18003 .2052124 133.5381
|
||||||
|
pair_coeff 1 1 0 .1 0
|
||||||
|
kspace_style ewald 1e-6
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
group type1 type 1
|
||||||
|
400 atoms in group type1
|
||||||
|
compute charge1 type1 property/atom q
|
||||||
|
compute q1 type1 reduce ave c_charge1
|
||||||
|
group type2 type 2
|
||||||
|
800 atoms in group type2
|
||||||
|
compute charge2 type2 property/atom q
|
||||||
|
compute q2 type2 reduce ave c_charge2
|
||||||
|
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
|
||||||
|
|
||||||
|
thermo_style custom step pe c_q1 c_q2 v_qtot
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
|
||||||
|
velocity all create 300.0 1281937
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
|
||||||
|
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
|
||||||
|
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
|
||||||
|
fix 2 all qeq/dynamic 1 10 1.0e-2 100 param.qeq2
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Ewald initialization ...
|
||||||
|
G vector (1/distance) = 0.305064
|
||||||
|
estimated absolute RMS force accuracy = 2.07629e-05
|
||||||
|
estimated relative force accuracy = 1.44191e-06
|
||||||
|
KSpace vectors: actual max1d max3d = 1696 10 4630
|
||||||
|
kxmax kymax kzmax = 9 9 10
|
||||||
|
Memory usage per processor = 11.8158 Mbytes
|
||||||
|
Step PotEng q1 q2 qtot
|
||||||
|
0 -15435.276 0.85155361 -0.4257768 1.9326762e-12
|
||||||
|
1 -15435.28 0.85155361 -0.4257768 1.9326762e-12
|
||||||
|
2 -15435.356 0.85155361 -0.4257768 1.9326762e-12
|
||||||
|
3 -15435.5 0.85155361 -0.4257768 1.9326762e-12
|
||||||
|
4 -15435.714 0.85155361 -0.4257768 1.9326762e-12
|
||||||
|
5 -15437.489 0.85191124 -0.42595562 1.4210855e-12
|
||||||
|
6 -15439.474 0.8523022 -0.4261511 1.1937118e-12
|
||||||
|
7 -15444.065 0.85330143 -0.42665072 1.5347723e-12
|
||||||
|
8 -15445.582 0.85354575 -0.42677288 1.4210855e-12
|
||||||
|
9 -15447.225 0.8538033 -0.42690165 1.6484591e-12
|
||||||
|
10 -15450.727 0.85448844 -0.42724422 1.6484591e-12
|
||||||
|
Loop time of 0.551397 on 1 procs for 10 steps with 1200 atoms
|
||||||
|
|
||||||
|
Pair time (%) = 0.190656 (34.5769)
|
||||||
|
Kspce time (%) = 0.293027 (53.1427)
|
||||||
|
Neigh time (%) = 0 (0)
|
||||||
|
Comm time (%) = 0.000636339 (0.115405)
|
||||||
|
Outpt time (%) = 0.000331879 (0.0601887)
|
||||||
|
Other time (%) = 0.0667453 (12.1048)
|
||||||
|
|
||||||
|
Nlocal: 1200 ave 1200 max 1200 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 8100 ave 8100 max 8100 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 367600 ave 367600 max 367600 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 367600
|
||||||
|
Ave neighs/atom = 306.333
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
@ -0,0 +1,85 @@
|
||||||
|
LAMMPS (5 Sep 2014)
|
||||||
|
# This example demonstrates the use of various fix qeq variants with
|
||||||
|
# that defines and uses charges, in this case pair_style buck/coul/long
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style charge
|
||||||
|
|
||||||
|
read_data data.aC
|
||||||
|
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
1200 atoms
|
||||||
|
|
||||||
|
pair_style buck/coul/long 12.0
|
||||||
|
pair_coeff 2 2 1388.77 .3623188 175.0
|
||||||
|
pair_coeff 1 2 18003 .2052124 133.5381
|
||||||
|
pair_coeff 1 1 0 .1 0
|
||||||
|
kspace_style ewald 1e-6
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
group type1 type 1
|
||||||
|
400 atoms in group type1
|
||||||
|
compute charge1 type1 property/atom q
|
||||||
|
compute q1 type1 reduce ave c_charge1
|
||||||
|
group type2 type 2
|
||||||
|
800 atoms in group type2
|
||||||
|
compute charge2 type2 property/atom q
|
||||||
|
compute q2 type2 reduce ave c_charge2
|
||||||
|
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
|
||||||
|
|
||||||
|
thermo_style custom step pe c_q1 c_q2 v_qtot
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
|
||||||
|
velocity all create 300.0 1281937
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
|
||||||
|
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
|
||||||
|
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
|
||||||
|
fix 2 all qeq/dynamic 1 10 1.0e-2 100 param.qeq2
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Ewald initialization ...
|
||||||
|
G vector (1/distance) = 0.305064
|
||||||
|
estimated absolute RMS force accuracy = 2.07629e-05
|
||||||
|
estimated relative force accuracy = 1.44191e-06
|
||||||
|
KSpace vectors: actual max1d max3d = 1696 10 4630
|
||||||
|
kxmax kymax kzmax = 9 9 10
|
||||||
|
Memory usage per processor = 7.02304 Mbytes
|
||||||
|
Step PotEng q1 q2 qtot
|
||||||
|
0 -15435.276 0.85155361 -0.4257768 -2.8421709e-13
|
||||||
|
1 -15435.28 0.85155361 -0.4257768 -2.8421709e-13
|
||||||
|
2 -15435.356 0.85155361 -0.4257768 -2.8421709e-13
|
||||||
|
3 -15435.5 0.85155361 -0.4257768 -2.8421709e-13
|
||||||
|
4 -15435.714 0.85155361 -0.4257768 -2.8421709e-13
|
||||||
|
5 -15437.489 0.85191124 -0.42595562 -1.1368684e-13
|
||||||
|
6 -15439.474 0.8523022 -0.4261511 -1.7053026e-13
|
||||||
|
7 -15444.065 0.85330143 -0.42665072 -1.7053026e-13
|
||||||
|
8 -15445.582 0.85354575 -0.42677288 -2.2737368e-13
|
||||||
|
9 -15447.225 0.8538033 -0.42690165 -2.2737368e-13
|
||||||
|
10 -15450.727 0.85448844 -0.42724422 0
|
||||||
|
Loop time of 0.144642 on 4 procs for 10 steps with 1200 atoms
|
||||||
|
|
||||||
|
Pair time (%) = 0.0504071 (34.8495)
|
||||||
|
Kspce time (%) = 0.0739903 (51.154)
|
||||||
|
Neigh time (%) = 0 (0)
|
||||||
|
Comm time (%) = 0.00123513 (0.85392)
|
||||||
|
Outpt time (%) = 0.00030756 (0.212635)
|
||||||
|
Other time (%) = 0.018702 (12.9299)
|
||||||
|
|
||||||
|
Nlocal: 300 ave 300 max 300 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 4875 ave 4880 max 4870 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 91900 ave 93081 max 90719 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 367600
|
||||||
|
Ave neighs/atom = 306.333
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
@ -0,0 +1,89 @@
|
||||||
|
LAMMPS (5 Sep 2014)
|
||||||
|
# This example demonstrates the use of various fix qeq variants with pair reax/c
|
||||||
|
# You can comment in/out various versions below
|
||||||
|
#
|
||||||
|
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
||||||
|
# used with pair_style reax/c, provided that the QEq parameters are the same.
|
||||||
|
#
|
||||||
|
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
||||||
|
# the QEq parameters are the same. These two styles can also be used with
|
||||||
|
# pair_style reax/c.
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style charge
|
||||||
|
|
||||||
|
read_data data.CHO
|
||||||
|
orthogonal box = (0 0 0) to (25 25 25)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
105 atoms
|
||||||
|
|
||||||
|
pair_style reax/c NULL checkqeq no
|
||||||
|
pair_coeff * * ffield.reax.cho H C O
|
||||||
|
|
||||||
|
neighbor 1 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
group type1 type 1
|
||||||
|
60 atoms in group type1
|
||||||
|
compute charge1 type1 property/atom q
|
||||||
|
compute q1 type1 reduce ave c_charge1
|
||||||
|
group type2 type 2
|
||||||
|
25 atoms in group type2
|
||||||
|
compute charge2 type2 property/atom q
|
||||||
|
compute q2 type2 reduce ave c_charge2
|
||||||
|
group type3 type 3
|
||||||
|
20 atoms in group type3
|
||||||
|
compute charge3 type3 property/atom q
|
||||||
|
compute q3 type3 reduce ave c_charge3
|
||||||
|
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
|
||||||
|
|
||||||
|
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
velocity all create 300.0 1281937
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
|
||||||
|
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
|
||||||
|
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
|
||||||
|
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
|
||||||
|
|
||||||
|
timestep 0.25
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Memory usage per processor = 15.3036 Mbytes
|
||||||
|
Step PotEng q1 q2 q3 qtot
|
||||||
|
0 -10226.557 0.095633908 -0.15658752 -0.091167326 3.1086245e-15
|
||||||
|
1 -10225.583 0.095556852 -0.15641218 -0.091155329 -3.5527137e-15
|
||||||
|
2 -10222.838 0.095491107 -0.15626315 -0.091144387 4.6629367e-15
|
||||||
|
3 -10218.529 0.095435139 -0.15613752 -0.091133515 4.8849813e-15
|
||||||
|
4 -10212.978 0.095388552 -0.15603364 -0.091123602 -1.110223e-15
|
||||||
|
5 -10206.591 0.095347264 -0.15594222 -0.091114022 -4.8849813e-15
|
||||||
|
6 -10199.824 0.095311447 -0.15586364 -0.091104787 2.6645353e-15
|
||||||
|
7 -10193.143 0.095275939 -0.15578522 -0.091096298 -8.8817842e-16
|
||||||
|
8 -10186.982 0.095240774 -0.15570734 -0.091088152 3.1086245e-15
|
||||||
|
9 -10181.712 0.095199169 -0.15561444 -0.091079454 0
|
||||||
|
10 -10177.608 0.09515654 -0.15551833 -0.091071711 -3.1086245e-15
|
||||||
|
Loop time of 0.028862 on 1 procs for 10 steps with 105 atoms
|
||||||
|
|
||||||
|
Pair time (%) = 0.023474 (81.3318)
|
||||||
|
Neigh time (%) = 0 (0)
|
||||||
|
Comm time (%) = 4.72069e-05 (0.163561)
|
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|
Outpt time (%) = 0.000179768 (0.622852)
|
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|
Other time (%) = 0.00516105 (17.8818)
|
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|
|
||||||
|
Nlocal: 105 ave 105 max 105 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 512 ave 512 max 512 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 3417 ave 3417 max 3417 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 3417
|
||||||
|
Ave neighs/atom = 32.5429
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
|
@ -0,0 +1,89 @@
|
||||||
|
LAMMPS (5 Sep 2014)
|
||||||
|
# This example demonstrates the use of various fix qeq variants with pair reax/c
|
||||||
|
# You can comment in/out various versions below
|
||||||
|
#
|
||||||
|
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
||||||
|
# used with pair_style reax/c, provided that the QEq parameters are the same.
|
||||||
|
#
|
||||||
|
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
||||||
|
# the QEq parameters are the same. These two styles can also be used with
|
||||||
|
# pair_style reax/c.
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style charge
|
||||||
|
|
||||||
|
read_data data.CHO
|
||||||
|
orthogonal box = (0 0 0) to (25 25 25)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
105 atoms
|
||||||
|
|
||||||
|
pair_style reax/c NULL checkqeq no
|
||||||
|
pair_coeff * * ffield.reax.cho H C O
|
||||||
|
|
||||||
|
neighbor 1 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
group type1 type 1
|
||||||
|
60 atoms in group type1
|
||||||
|
compute charge1 type1 property/atom q
|
||||||
|
compute q1 type1 reduce ave c_charge1
|
||||||
|
group type2 type 2
|
||||||
|
25 atoms in group type2
|
||||||
|
compute charge2 type2 property/atom q
|
||||||
|
compute q2 type2 reduce ave c_charge2
|
||||||
|
group type3 type 3
|
||||||
|
20 atoms in group type3
|
||||||
|
compute charge3 type3 property/atom q
|
||||||
|
compute q3 type3 reduce ave c_charge3
|
||||||
|
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
|
||||||
|
|
||||||
|
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
velocity all create 300.0 1281937
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
|
||||||
|
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
|
||||||
|
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
|
||||||
|
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
|
||||||
|
|
||||||
|
timestep 0.25
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Memory usage per processor = 11.1055 Mbytes
|
||||||
|
Step PotEng q1 q2 q3 qtot
|
||||||
|
0 -10226.557 0.095633887 -0.15658751 -0.091167271 -1.110223e-15
|
||||||
|
1 -10225.583 0.095556773 -0.15641189 -0.09115546 -4.4408921e-16
|
||||||
|
2 -10222.838 0.095491109 -0.15626315 -0.091144385 -1.3322676e-15
|
||||||
|
3 -10218.529 0.095435154 -0.15613758 -0.091133492 -4.4408921e-16
|
||||||
|
4 -10212.978 0.095388557 -0.15603363 -0.091123632 -1.7763568e-15
|
||||||
|
5 -10206.591 0.095347386 -0.15594266 -0.091113837 1.110223e-15
|
||||||
|
6 -10199.824 0.095311782 -0.1558644 -0.09110485 -1.110223e-15
|
||||||
|
7 -10193.143 0.095275616 -0.15578453 -0.091096188 -4.4408921e-16
|
||||||
|
8 -10186.982 0.09524102 -0.15570787 -0.091088227 -1.3322676e-15
|
||||||
|
9 -10181.712 0.095199505 -0.15561531 -0.09107938 4.4408921e-16
|
||||||
|
10 -10177.608 0.095156459 -0.15551826 -0.091071551 3.9968029e-15
|
||||||
|
Loop time of 0.0162442 on 4 procs for 10 steps with 105 atoms
|
||||||
|
|
||||||
|
Pair time (%) = 0.0100933 (62.1349)
|
||||||
|
Neigh time (%) = 0 (0)
|
||||||
|
Comm time (%) = 0.00139159 (8.56667)
|
||||||
|
Outpt time (%) = 0.000339925 (2.09259)
|
||||||
|
Other time (%) = 0.00441939 (27.2059)
|
||||||
|
|
||||||
|
Nlocal: 26.25 ave 35 max 15 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||||
|
Nghost: 300 ave 357 max 239 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 1025.25 ave 1468 max 405 min
|
||||||
|
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 4101
|
||||||
|
Ave neighs/atom = 39.0571
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
|
@ -0,0 +1,3 @@
|
||||||
|
1 5.3200 14.8732 1.0206
|
||||||
|
2 5.8678 14.0000 0.9000
|
||||||
|
3 8.5000 17.9978 1.0503
|
||||||
|
|
@ -0,0 +1,4 @@
|
||||||
|
real
|
||||||
|
1 5.3200 14.8732 1.0206 0.0 0.0
|
||||||
|
2 5.8678 14.0000 0.9000 0.0 0.0
|
||||||
|
3 8.5000 17.9978 1.0503 0.0 0.0
|
||||||
|
|
@ -0,0 +1,3 @@
|
||||||
|
metal
|
||||||
|
1 0.00000 7.25028 0.01 0.772871 0.000000
|
||||||
|
2 11.26882 15.37920 0.01 0.243072 0.000000
|
||||||
Loading…
Reference in New Issue