forked from lijiext/lammps
proper handle partial initialization from infile
This commit is contained in:
Axel Kohlmeyer
parent
89c7d8f707
commit
550ae15dff
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@ -0,0 +1,7 @@
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# set fix rigid mass, COM, inertia tensor info for 4 of the 9 bodies
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4
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2 9.0000000000000000e+00 1.6111111111111112e+00 1.7222222222222223e+00 1.1111111111111110e-01 3.9444444444444442e+00 2.2777777777777772e+00 4.4444444444444438e+00 -2.7777777777777757e-01 1.1111111111111105e-01 2.2222222222222235e-01 4.3171479957811609e+00 -1.0618113255001780e+00 -1.8643700998325481e+00 4.5148932178264438e+00 1.0733638777335948e+01 9.1950804203772858e+00 0 0 0
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3 9.0000000000000000e+00 2.8333333333333335e+00 2.7222222222222223e+00 1.1111111111111110e-01 3.9444444444444446e+00 3.3888888888888902e+00 5.5555555555555562e+00 -8.3333333333333415e-01 3.3333333333333304e-01 2.2222222222222254e-01 1.6315473697148597e-01 -7.2705885868299369e-01 5.5332911778921119e+00 -1.5846021643158503e+01 6.3829570883561679e+00 -4.3451481846875879e+01 0 0 0
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5 9.0000000000000000e+00 5.1111111111111107e+00 5.0000000000000000e+00 1.1111111111111110e-01 4.3888888888888911e+00 2.7777777777777790e+00 5.3888888888888919e+00 -7.5000000000000056e-01 6.1111111111111172e-01 5.0000000000000022e-01 -5.9985136455141390e+00 3.8759047575157033e+00 -2.0802380702072480e+00 -9.6671050263449843e+00 -2.3012986946431408e+01 -2.3443650645115170e+01 0 0 0
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9 9.0000000000000000e+00 9.5000000000000000e+00 9.5000000000000000e+00 1.1111111111111110e-01 2.3888888888888893e+00 2.3888888888888888e+00 3.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.8008148769529069e+00 -2.6284193340862787e+00 -3.3758037136596228e+00 -1.1454679561601873e+01 2.8578517607187521e+01 -2.0466336627273300e+01 0 0 0
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@ -1,7 +1,7 @@
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# LAMMPS data file for rigid bodies
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81 atoms
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1 atom types
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81 atoms
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1 atom types
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-12 12 xlo xhi
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-12 12 ylo yhi
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@ -17,84 +17,84 @@ Pair Coeffs
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Atoms
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1 1 0 0 0
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2 1 0 1 0
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3 1 0 0.5 0
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4 1 0.5 0 0
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5 1 0.5 0.5 1
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6 1 1 0.5 0
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7 1 0.5 1 0
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8 1 1 0 0
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9 1 1 1 0
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10 1 2 1 0
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11 1 1 2 0
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12 1 1.5 2 0
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13 1 1.5 1 0
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14 1 1 1.5 0
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15 1 1.5 1.5 1
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16 1 2 1.5 0
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17 1 2 2 0
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18 1 2 3 0
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19 1 2 2.5 0
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20 1 2.5 2 0
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21 1 2.5 2.5 1
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22 1 3 2.5 0
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23 1 2.5 3 0
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24 1 3 2 0
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25 1 3 3 0
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26 1 4 3 0
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27 1 3 4 0
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28 1 3.5 4 0
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29 1 3.5 3 0
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30 1 3 3.5 0
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31 1 3.5 3.5 1
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32 1 4 3.5 0
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33 1 4 4 0
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34 1 4 5 0
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35 1 4 4.5 0
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36 1 4.5 4 0
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37 1 4.5 4.5 1
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38 1 5 4.5 0
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39 1 4.5 5 0
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40 1 5 4 0
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41 1 5 5 0
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42 1 6 5 0
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43 1 5 6 0
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44 1 5.5 6 0
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45 1 5.5 5 0
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46 1 5 5.5 0
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47 1 5.5 5.5 1
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48 1 6 5.5 0
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49 1 6 6 0
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50 1 6 7 0
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51 1 6 6.5 0
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52 1 6.5 6 0
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53 1 6.5 6.5 1
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54 1 7 6.5 0
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55 1 6.5 7 0
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56 1 7 6 0
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57 1 7 7 0
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58 1 8 7 0
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59 1 7 8 0
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60 1 7.5 8 0
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61 1 7.5 7 0
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62 1 7 7.5 0
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63 1 7.5 7.5 1
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64 1 8 7.5 0
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65 1 8 8 0
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66 1 8 9 0
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67 1 8 8.5 0
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68 1 8.5 8 0
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69 1 8.5 8.5 1
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70 1 9 8.5 0
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71 1 8.5 9 0
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72 1 9 8 0
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73 1 9 9 0
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74 1 10 9 0
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75 1 9 10 0
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76 1 9.5 10 0
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77 1 9.5 9 0
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78 1 9 9.5 0
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79 1 9.5 9.5 1
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80 1 10 9.5 0
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81 1 10 10 0
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1 1 0 0 0
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2 1 0 1 0
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3 1 0 0.5 0
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4 1 0.5 0 0
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5 1 0.5 0.5 1
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6 1 1 0.5 0
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7 1 0.5 1 0
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8 1 1 0 0
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9 1 1 1 0
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10 1 2 1 0
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11 1 1 2 0
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12 1 1.5 2 0
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13 1 1.5 1 0
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14 1 1 1.5 0
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15 1 1.5 1.5 1
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16 1 2 1.5 0
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17 1 2 2 0
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18 1 2 3 0
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19 1 2 2.5 0
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20 1 2.5 2 0
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21 1 2.5 2.5 1
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22 1 3 2.5 0
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23 1 2.5 3 0
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24 1 3 2 0
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25 1 3 3 0
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26 1 4 3 0
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27 1 3 4 0
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28 1 3.5 4 0
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29 1 3.5 3 0
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30 1 3 3.5 0
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31 1 3.5 3.5 1
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32 1 4 3.5 0
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33 1 4 4 0
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34 1 4 5 0
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35 1 4 4.5 0
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36 1 4.5 4 0
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37 1 4.5 4.5 1
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38 1 5 4.5 0
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39 1 4.5 5 0
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40 1 5 4 0
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41 1 5 5 0
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42 1 6 5 0
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43 1 5 6 0
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44 1 5.5 6 0
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45 1 5.5 5 0
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46 1 5 5.5 0
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47 1 5.5 5.5 1
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48 1 6 5.5 0
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49 1 6 6 0
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50 1 6 7 0
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51 1 6 6.5 0
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52 1 6.5 6 0
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53 1 6.5 6.5 1
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54 1 7 6.5 0
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55 1 6.5 7 0
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56 1 7 6 0
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57 1 7 7 0
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58 1 8 7 0
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59 1 7 8 0
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60 1 7.5 8 0
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61 1 7.5 7 0
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62 1 7 7.5 0
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63 1 7.5 7.5 1
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64 1 8 7.5 0
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65 1 8 8 0
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66 1 8 9 0
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67 1 8 8.5 0
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68 1 8.5 8 0
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69 1 8.5 8.5 1
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70 1 9 8.5 0
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71 1 8.5 9 0
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72 1 9 8 0
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73 1 9 9 0
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74 1 10 9 0
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75 1 9 10 0
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76 1 9.5 10 0
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77 1 9.5 9 0
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78 1 9 9.5 0
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79 1 9.5 9.5 1
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80 1 10 9.5 0
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81 1 10 10 0
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@ -0,0 +1,100 @@
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# LAMMPS data file for rigid bodies
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81 atoms
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1 atom types
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-12 12 xlo xhi
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-12 12 ylo yhi
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-12 12 zlo zhi
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Masses
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1 1
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Pair Coeffs
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1 1 1
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Atoms
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1 1 1 0 0 0
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2 1 1 0 1 0
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3 1 1 0 0.5 0
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4 1 1 0.5 0 0
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5 1 1 0.5 0.5 1
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6 1 1 1 0.5 0
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7 1 1 0.5 1 0
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8 1 1 1 0 0
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9 1 1 1 1 0
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10 2 1 2 1 0
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11 2 1 1 2 0
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12 2 1 1.5 2 0
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13 2 1 1.5 1 0
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14 2 1 1 1.5 0
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15 2 1 1.5 1.5 1
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16 2 1 2 1.5 0
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17 2 1 2 2 0
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18 2 1 2 3 0
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19 3 1 2 2.5 0
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20 3 1 2.5 2 0
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21 3 1 2.5 2.5 1
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22 3 1 3 2.5 0
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23 3 1 2.5 3 0
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24 3 1 3 2 0
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25 3 1 3 3 0
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26 3 1 4 3 0
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27 3 1 3 4 0
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28 4 1 3.5 4 0
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29 4 1 3.5 3 0
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30 4 1 3 3.5 0
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31 4 1 3.5 3.5 1
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32 4 1 4 3.5 0
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33 4 1 4 4 0
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34 4 1 4 5 0
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35 4 1 4 4.5 0
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36 4 1 4.5 4 0
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37 5 1 4.5 4.5 1
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38 5 1 5 4.5 0
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39 5 1 4.5 5 0
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40 5 1 5 4 0
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41 5 1 5 5 0
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42 5 1 6 5 0
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43 5 1 5 6 0
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44 5 1 5.5 6 0
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45 5 1 5.5 5 0
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46 6 1 5 5.5 0
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47 6 1 5.5 5.5 1
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48 6 1 6 5.5 0
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49 6 1 6 6 0
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50 6 1 6 7 0
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51 6 1 6 6.5 0
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52 6 1 6.5 6 0
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53 6 1 6.5 6.5 1
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54 6 1 7 6.5 0
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55 7 1 6.5 7 0
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56 7 1 7 6 0
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57 7 1 7 7 0
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58 7 1 8 7 0
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59 7 1 7 8 0
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60 7 1 7.5 8 0
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61 7 1 7.5 7 0
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62 7 1 7 7.5 0
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63 7 1 7.5 7.5 1
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64 8 1 8 7.5 0
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65 8 1 8 8 0
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66 8 1 8 9 0
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67 8 1 8 8.5 0
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68 8 1 8.5 8 0
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69 8 1 8.5 8.5 1
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70 8 1 9 8.5 0
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71 8 1 8.5 9 0
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72 8 1 9 8 0
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73 9 1 9 9 0
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74 9 1 10 9 0
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75 9 1 9 10 0
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76 9 1 9.5 10 0
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77 9 1 9.5 9 0
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78 9 1 9 9.5 0
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79 9 1 9.5 9.5 1
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80 9 1 10 9.5 0
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81 9 1 10 10 0
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@ -1,81 +1,81 @@
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# Simple rigid body system
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units lj
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atom_style atomic
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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pair_style lj/cut 2.5
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read_data data.rigid
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read_data data.rigid
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velocity all create 100.0 4928459
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velocity all create 100.0 4928459
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# unconnected bodies
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group clump1 id <> 1 9
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group clump2 id <> 10 18
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group clump3 id <> 19 27
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group clump4 id <> 28 36
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group clump5 id <> 37 45
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group clump6 id <> 46 54
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group clump7 id <> 55 63
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group clump8 id <> 64 72
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group clump9 id <> 73 81
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group clump1 id <> 1 9
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group clump2 id <> 10 18
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group clump3 id <> 19 27
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group clump4 id <> 28 36
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group clump5 id <> 37 45
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group clump6 id <> 46 54
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group clump7 id <> 55 63
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group clump8 id <> 64 72
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group clump9 id <> 73 81
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fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
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clump6 clump7 clump8 clump9
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clump6 clump7 clump8 clump9
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# 1 chain of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 36 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 36 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
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# clump6 clump7 clump8 clump9
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# clump6 clump7 clump8 clump9
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# 2 chains of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 37 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 37 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4
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#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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thermo 100
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#dump 1 all atom 50 dump.rigid
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#dump 1 all atom 50 dump.rigid
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#dump 2 all image 100 image.*.jpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 2 all image 100 image.*.jpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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#dump 3 all movie 100 movie.mpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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timestep 0.0001
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thermo 50
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run 10000
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@ -0,0 +1,52 @@
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# Simple rigid body system
|
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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read_data data.rigid
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velocity all create 100.0 4928459
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# unconnected bodies
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group clump1 id <> 1 9
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group clump2 id <> 10 18
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group clump3 id <> 19 27
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group clump4 id <> 28 36
|
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group clump5 id <> 37 45
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group clump6 id <> 46 54
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group clump7 id <> 55 63
|
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group clump8 id <> 64 72
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group clump9 id <> 73 81
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fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
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clump6 clump7 clump8 clump9 &
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infile bodyinfo.dat
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|
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neigh_modify exclude group clump1 clump1
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||||
neigh_modify exclude group clump2 clump2
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||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
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neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid
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#dump 2 all image 100 image.*.jpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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|
||||
#dump 3 all movie 100 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 10 18
|
||||
group clump3 id <> 19 27
|
||||
group clump4 id <> 28 36
|
||||
group clump5 id <> 37 45
|
||||
group clump6 id <> 46 54
|
||||
group clump7 id <> 55 63
|
||||
group clump8 id <> 64 72
|
||||
group clump9 id <> 73 81
|
||||
|
||||
fix 1 all rigid molecule
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 10 18
|
||||
group clump3 id <> 19 27
|
||||
group clump4 id <> 28 36
|
||||
group clump5 id <> 37 45
|
||||
group clump6 id <> 46 54
|
||||
group clump7 id <> 55 63
|
||||
group clump8 id <> 64 72
|
||||
group clump9 id <> 73 81
|
||||
|
||||
fix 1 all rigid/small molecule
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 10 18
|
||||
group clump3 id <> 19 27
|
||||
group clump4 id <> 28 36
|
||||
group clump5 id <> 37 45
|
||||
group clump6 id <> 46 54
|
||||
group clump7 id <> 55 63
|
||||
group clump8 id <> 64 72
|
||||
group clump9 id <> 73 81
|
||||
|
||||
fix 1 all rigid/small molecule infile bodyinfo.dat
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,312 @@
|
|||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Reading rigid body data for 4 bodies from file bodyinfo.dat
|
||||
Reading rigid body data for 4 bodies from file bodyinfo.dat
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722793e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06941 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156167 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.02681437 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191524 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589895 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550156 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620325 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270436 0 5269.5237 11.395099
|
||||
9900 16738.489 -0.0002498452 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395077
|
||||
10000 16738.49 0 0 5269.5246 11.395076
|
||||
Loop time of 0.0882903 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 978589.581 tau/day, 113262.683 timesteps/s
|
||||
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0064583 | 0.0064583 | 0.0064583 | 0.0 | 7.31
|
||||
Neigh | 0.027186 | 0.027186 | 0.027186 | 0.0 | 30.79
|
||||
Comm | 0.0057041 | 0.0057041 | 0.0057041 | 0.0 | 6.46
|
||||
Output | 0.0020628 | 0.0020628 | 0.0020628 | 0.0 | 2.34
|
||||
Modify | 0.042816 | 0.042816 | 0.042816 | 0.0 | 48.49
|
||||
Other | | 0.004063 | | | 4.60
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,312 @@
|
|||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Reading rigid body data for 4 bodies from file bodyinfo.dat
|
||||
Reading rigid body data for 4 bodies from file bodyinfo.dat
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.972279e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06941 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.004530741 0 5269.5178 12.01162
|
||||
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156168 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191524 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589899 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550149 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620325 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270428 0 5269.5237 11.395099
|
||||
9900 16738.489 -0.0002498452 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395077
|
||||
10000 16738.49 0 0 5269.5246 11.395076
|
||||
Loop time of 0.100422 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 860368.209 tau/day, 99579.654 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 | 0.0014853 | 0.0020649 | 0.0026245 | 0.9 | 2.06
|
||||
Neigh | 0.0075956 | 0.0080256 | 0.0091971 | 0.8 | 7.99
|
||||
Comm | 0.037221 | 0.041059 | 0.043195 | 1.2 | 40.89
|
||||
Output | 0.0020995 | 0.0023594 | 0.003073 | 0.8 | 2.35
|
||||
Modify | 0.041318 | 0.042855 | 0.044215 | 0.5 | 42.67
|
||||
Other | | 0.004059 | | | 4.04
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,349 @@
|
|||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid molecule
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.97228e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06941 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156166 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191524 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589897 0 5269.4979 12.062708
|
||||
9750 16738.013 0.1355014 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620325 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270449 0 5269.5237 11.395099
|
||||
9900 16738.489 -0.00024984529 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395077
|
||||
10000 16738.49 0 0 5269.5246 11.395076
|
||||
Loop time of 0.0974108 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 886965.415 tau/day, 102658.034 timesteps/s
|
||||
96.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0068054 | 0.0068054 | 0.0068054 | 0.0 | 6.99
|
||||
Bond | 0.00034618 | 0.00034618 | 0.00034618 | 0.0 | 0.36
|
||||
Neigh | 0.033076 | 0.033076 | 0.033076 | 0.0 | 33.96
|
||||
Comm | 0.0067938 | 0.0067938 | 0.0067938 | 0.0 | 6.97
|
||||
Output | 0.0022905 | 0.0022905 | 0.0022905 | 0.0 | 2.35
|
||||
Modify | 0.044027 | 0.044027 | 0.044027 | 0.0 | 45.20
|
||||
Other | | 0.004071 | | | 4.18
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,349 @@
|
|||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid molecule
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.08 | 5.112 | 5.206 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722775e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706556 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06941 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690662 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.004530741 0 5269.5178 12.01162
|
||||
8600 16738.474 -0.00076532815 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652439 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156171 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814373 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191525 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589908 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550139 0 5269.5101 11.407247
|
||||
9800 16738.512 -0.011620323 0 5269.5201 11.394975
|
||||
9850 16738.489 -0.00067270407 0 5269.5237 11.395099
|
||||
9900 16738.489 -0.00024984518 0 5269.5242 11.395086
|
||||
9950 16738.49 0 0 5269.5245 11.395077
|
||||
10000 16738.49 0 0 5269.5246 11.395076
|
||||
Loop time of 0.102079 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 846406.333 tau/day, 97963.696 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0015357 | 0.0020418 | 0.0024561 | 0.7 | 2.00
|
||||
Bond | 0.00030031 | 0.00031957 | 0.00034464 | 0.0 | 0.31
|
||||
Neigh | 0.0091719 | 0.0094934 | 0.010243 | 0.4 | 9.30
|
||||
Comm | 0.038015 | 0.041242 | 0.043481 | 1.1 | 40.40
|
||||
Output | 0.002223 | 0.0024412 | 0.0030738 | 0.7 | 2.39
|
||||
Modify | 0.040725 | 0.042557 | 0.043982 | 0.7 | 41.69
|
||||
Other | | 0.003983 | | | 3.90
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,322 @@
|
|||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid/small molecule
|
||||
create bodies CPU = 0.000 seconds
|
||||
9 rigid bodies with 81 atoms
|
||||
1.2247449 = max distance from body owner to body atom
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722826e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.255443 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585966 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693235 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.05932751 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.092031
|
||||
3550 16713.405 7.8460623 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663192 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934371 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706562 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253348 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690678 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646809 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307407 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532803 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.0003765242 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156153 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814361 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.1019152 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589855 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550223 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.01162033 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.000672705 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984511 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395077
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.097001 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 890712.494 tau/day, 103091.724 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 | 0.0064264 | 0.0064264 | 0.0064264 | 0.0 | 6.63
|
||||
Bond | 0.0003385 | 0.0003385 | 0.0003385 | 0.0 | 0.35
|
||||
Neigh | 0.030894 | 0.030894 | 0.030894 | 0.0 | 31.85
|
||||
Comm | 0.0065732 | 0.0065732 | 0.0065732 | 0.0 | 6.78
|
||||
Output | 0.0021773 | 0.0021773 | 0.0021773 | 0.0 | 2.24
|
||||
Modify | 0.046477 | 0.046477 | 0.046477 | 0.0 | 47.91
|
||||
Other | | 0.004115 | | | 4.24
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,322 @@
|
|||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid/small molecule
|
||||
create bodies CPU = 0.000 seconds
|
||||
9 rigid bodies with 81 atoms
|
||||
1.2247449 = max distance from body owner to body atom
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.972281e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156165 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.02681437 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||
9750 16738.013 0.1355014 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620326 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270465 0 5269.5237 11.395099
|
||||
9900 16738.489 -0.00024984533 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395077
|
||||
10000 16738.49 0 0 5269.5246 11.395076
|
||||
Loop time of 0.115632 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 747196.558 tau/day, 86481.083 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0014528 | 0.0020376 | 0.0024938 | 0.9 | 1.76
|
||||
Bond | 0.00030255 | 0.00030731 | 0.00031718 | 0.0 | 0.27
|
||||
Neigh | 0.0089963 | 0.0094964 | 0.010494 | 0.6 | 8.21
|
||||
Comm | 0.035947 | 0.038848 | 0.040951 | 1.0 | 33.60
|
||||
Output | 0.0022924 | 0.002542 | 0.0032643 | 0.8 | 2.20
|
||||
Modify | 0.056743 | 0.058255 | 0.059447 | 0.4 | 50.38
|
||||
Other | | 0.004146 | | | 3.59
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,323 @@
|
|||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid/small molecule infile bodyinfo.dat
|
||||
create bodies CPU = 0.000 seconds
|
||||
9 rigid bodies with 81 atoms
|
||||
1.2247449 = max distance from body owner to body atom
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Reading rigid body data for 4 bodies from file bodyinfo.dat
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722817e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.05932751 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934369 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706559 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690668 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646805 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652432 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814368 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589884 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550153 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620327 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270481 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984532 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395077
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.0973982 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 887079.894 tau/day, 102671.284 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 | 0.0065928 | 0.0065928 | 0.0065928 | 0.0 | 6.77
|
||||
Bond | 0.00033457 | 0.00033457 | 0.00033457 | 0.0 | 0.34
|
||||
Neigh | 0.031245 | 0.031245 | 0.031245 | 0.0 | 32.08
|
||||
Comm | 0.0065444 | 0.0065444 | 0.0065444 | 0.0 | 6.72
|
||||
Output | 0.0024004 | 0.0024004 | 0.0024004 | 0.0 | 2.46
|
||||
Modify | 0.045966 | 0.045966 | 0.045966 | 0.0 | 47.19
|
||||
Other | | 0.004315 | | | 4.43
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,323 @@
|
|||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid.small
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid/small molecule infile bodyinfo.dat
|
||||
create bodies CPU = 0.000 seconds
|
||||
9 rigid bodies with 81 atoms
|
||||
1.2247449 = max distance from body owner to body atom
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Reading rigid body data for 4 bodies from file bodyinfo.dat
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722791e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585966 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.05932751 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460622 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663193 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934369 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706559 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690669 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646806 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532809 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.0003765243 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156164 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814368 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589884 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550185 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620326 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270434 0 5269.5237 11.395099
|
||||
9900 16738.489 -0.00024984508 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395077
|
||||
10000 16738.49 0 0 5269.5246 11.395076
|
||||
Loop time of 0.135757 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 636433.251 tau/day, 73661.256 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0020781 | 0.0024716 | 0.0032187 | 0.9 | 1.82
|
||||
Bond | 0.00029013 | 0.000332 | 0.00037076 | 0.0 | 0.24
|
||||
Neigh | 0.0087772 | 0.011705 | 0.014134 | 2.3 | 8.62
|
||||
Comm | 0.042702 | 0.045012 | 0.048023 | 1.1 | 33.16
|
||||
Output | 0.0027373 | 0.0030292 | 0.0036178 | 0.6 | 2.23
|
||||
Modify | 0.067437 | 0.068617 | 0.069634 | 0.3 | 50.54
|
||||
Other | | 0.004589 | | | 3.38
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -134,11 +134,9 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
int is_double,cols;
|
||||
int custom_index = atom->find_custom(arg[4]+2,is_double,cols);
|
||||
if (custom_index == -1)
|
||||
error->all(FLERR,"Fix rigid custom requires "
|
||||
"previously defined property/atom");
|
||||
error->all(FLERR,"Fix rigid custom requires previously defined property/atom");
|
||||
else if (is_double)
|
||||
error->all(FLERR,"Fix rigid custom requires "
|
||||
"integer-valued property/atom vector");
|
||||
error->all(FLERR,"Fix rigid custom requires integer-valued property/atom vector");
|
||||
int minval = INT_MAX;
|
||||
int *value = atom->ivector[custom_index];
|
||||
for (i = 0; i < nlocal; i++)
|
||||
|
|
@ -155,9 +153,9 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
} else if (utils::strmatch(arg[4],"^v_")) {
|
||||
int ivariable = input->variable->find(arg[4]+2);
|
||||
if (ivariable < 0)
|
||||
error->all(FLERR,"Variable name for fix rigid custom does not exist");
|
||||
error->all(FLERR,"Variable {} for fix rigid/small custom does not exist", arg[4]+2);
|
||||
if (input->variable->atomstyle(ivariable) == 0)
|
||||
error->all(FLERR,"Fix rigid custom variable is no atom-style variable");
|
||||
error->all(FLERR,"Fix rigid custom variable {} is not atom-style variable", arg[4]+2);
|
||||
double *value = new double[nlocal];
|
||||
input->variable->compute_atom(ivariable,0,value,1,0);
|
||||
int minval = INT_MAX;
|
||||
|
|
@ -218,7 +216,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
}
|
||||
|
||||
memory->destroy(ncount);
|
||||
if (custom_flag) delete [] molecule;
|
||||
if (custom_flag) delete[] molecule;
|
||||
|
||||
// each listed group is a rigid body
|
||||
// check if all listed groups exist
|
||||
|
|
@ -259,7 +257,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (flagall)
|
||||
error->all(FLERR,"One or more atoms belong to multiple rigid bodies");
|
||||
|
||||
delete [] igroups;
|
||||
delete[] igroups;
|
||||
|
||||
} else error->all(FLERR,"Illegal fix rigid command");
|
||||
|
||||
|
|
@ -502,7 +500,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
|
||||
else {
|
||||
allremap = 0;
|
||||
delete [] id_dilate;
|
||||
delete[] id_dilate;
|
||||
id_dilate = utils::strdup(arg[iarg+1]);
|
||||
int idilate = group->find(id_dilate);
|
||||
if (idilate == -1)
|
||||
|
|
@ -529,7 +527,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
} else if (strcmp(arg[iarg],"infile") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
|
||||
delete [] inpfile;
|
||||
delete[] inpfile;
|
||||
inpfile = utils::strdup(arg[iarg+1]);
|
||||
restart_file = 1;
|
||||
reinitflag = 0;
|
||||
|
|
@ -542,7 +540,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
} else if (strcmp(arg[iarg],"gravity") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
|
||||
delete [] id_gravity;
|
||||
delete[] id_gravity;
|
||||
id_gravity = utils::strdup(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
|
||||
|
|
@ -584,7 +582,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (body[i] >= 0) ncount[body[i]]++;
|
||||
|
||||
MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world);
|
||||
delete [] ncount;
|
||||
delete[] ncount;
|
||||
|
||||
for (ibody = 0; ibody < nbody; ibody++)
|
||||
if (nrigid[ibody] <= 1) error->all(FLERR,"One or zero atoms in rigid body");
|
||||
|
|
@ -615,9 +613,9 @@ FixRigid::~FixRigid()
|
|||
atom->delete_callback(id,Atom::GROW);
|
||||
|
||||
delete random;
|
||||
delete [] inpfile;
|
||||
delete [] id_dilate;
|
||||
delete [] id_gravity;
|
||||
delete[] inpfile;
|
||||
delete[] id_dilate;
|
||||
delete[] id_gravity;
|
||||
|
||||
memory->destroy(mol2body);
|
||||
memory->destroy(body2mol);
|
||||
|
|
@ -674,8 +672,6 @@ int FixRigid::setmask()
|
|||
|
||||
void FixRigid::init()
|
||||
{
|
||||
int i,ibody;
|
||||
|
||||
triclinic = domain->triclinic;
|
||||
|
||||
// atom style pointers to particles that store extra info
|
||||
|
|
@ -688,18 +684,16 @@ void FixRigid::init()
|
|||
// if earlyflag, warn if any post-force fixes come after a rigid fix
|
||||
|
||||
int count = 0;
|
||||
for (i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->rigid_flag) count++;
|
||||
for (auto ifix : modify->get_fix_list())
|
||||
if (ifix->rigid_flag) count++;
|
||||
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
|
||||
|
||||
if (earlyflag) {
|
||||
int rflag = 0;
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (modify->fix[i]->rigid_flag) rflag = 1;
|
||||
if (rflag && (modify->fmask[i] & POST_FORCE) &&
|
||||
!modify->fix[i]->rigid_flag)
|
||||
error->warning(FLERR,"Fix {} alters forces after fix rigid",
|
||||
modify->fix[i]->id);
|
||||
bool rflag = false;
|
||||
for (auto ifix : modify->get_fix_list()) {
|
||||
if (ifix->rigid_flag) rflag = true;
|
||||
if ((comm->me == 0) && rflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
|
||||
error->warning(FLERR,"Fix {} alters forces after fix rigid", ifix->id);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -709,36 +703,30 @@ void FixRigid::init()
|
|||
// and gravity is not applied correctly
|
||||
|
||||
if (inpfile && !id_gravity) {
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (strcmp(modify->fix[i]->style,"gravity") == 0) {
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Gravity may not be correctly applied "
|
||||
"to rigid bodies if they consist of "
|
||||
"overlapped particles");
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (modify->get_fix_by_style("^gravity").size() > 0)
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Gravity may not be correctly applied to rigid "
|
||||
"bodies if they consist of overlapped particles");
|
||||
}
|
||||
|
||||
// error if a fix changing the box comes before rigid fix
|
||||
|
||||
for (i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->box_change) break;
|
||||
if (i < modify->nfix) {
|
||||
for (int j = i+1; j < modify->nfix; j++)
|
||||
if (utils::strmatch(modify->fix[j]->style,"^rigid"))
|
||||
bool boxflag = false;
|
||||
for (auto ifix : modify->get_fix_list()) {
|
||||
if (ifix->box_change) boxflag = true;
|
||||
if (boxflag && utils::strmatch(ifix->style,"^rigid"))
|
||||
error->all(FLERR,"Rigid fixes must come before any box changing fix");
|
||||
}
|
||||
|
||||
// add gravity forces based on gravity vector from fix
|
||||
|
||||
if (id_gravity) {
|
||||
int ifix = modify->find_fix(id_gravity);
|
||||
if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");
|
||||
if (!utils::strmatch(modify->fix[ifix]->style,"^gravity"))
|
||||
error->all(FLERR,"Fix rigid gravity fix ID is not a gravity fix style");
|
||||
auto ifix = modify->get_fix_by_id(id_gravity);
|
||||
if (!ifix) error->all(FLERR,"Fix rigid cannot find fix gravity ID {}", id_gravity);
|
||||
if (!utils::strmatch(ifix->style,"^gravity"))
|
||||
error->all(FLERR,"Fix rigid gravity fix ID {} is not a gravity fix style", id_gravity);
|
||||
int tmp;
|
||||
gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
|
||||
gvec = (double *) ifix->extract("gvec", tmp);
|
||||
}
|
||||
|
||||
// timestep info
|
||||
|
|
@ -767,7 +755,7 @@ void FixRigid::init()
|
|||
// temperature scale factor
|
||||
|
||||
double ndof = 0.0;
|
||||
for (ibody = 0; ibody < nbody; ibody++) {
|
||||
for (int ibody = 0; ibody < nbody; ibody++) {
|
||||
ndof += fflag[ibody][0] + fflag[ibody][1] + fflag[ibody][2];
|
||||
ndof += tflag[ibody][0] + tflag[ibody][1] + tflag[ibody][2];
|
||||
}
|
||||
|
|
@ -1237,7 +1225,7 @@ int FixRigid::dof(int tgroup)
|
|||
if (!setupflag) {
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Cannot count rigid body degrees-of-freedom "
|
||||
"before bodies are initialized");
|
||||
"before bodies are fully initialized");
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
|
@ -1307,10 +1295,10 @@ int FixRigid::dof(int tgroup)
|
|||
n += 2*nall[ibody] + 3*mall[ibody] - 3;
|
||||
}
|
||||
|
||||
delete [] ncount;
|
||||
delete [] mcount;
|
||||
delete [] nall;
|
||||
delete [] mall;
|
||||
delete[] ncount;
|
||||
delete[] mcount;
|
||||
delete[] nall;
|
||||
delete[] mall;
|
||||
|
||||
return n;
|
||||
}
|
||||
|
|
@ -1397,12 +1385,9 @@ void FixRigid::set_xv()
|
|||
MathExtra::matvec(ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody],displace[i],x[i]);
|
||||
|
||||
v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] +
|
||||
vcm[ibody][0];
|
||||
v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] +
|
||||
vcm[ibody][1];
|
||||
v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] +
|
||||
vcm[ibody][2];
|
||||
v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] + vcm[ibody][0];
|
||||
v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] + vcm[ibody][1];
|
||||
v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] + vcm[ibody][2];
|
||||
|
||||
// add center of mass to displacement
|
||||
// map back into periodic box via xbox,ybox,zbox
|
||||
|
|
@ -1555,12 +1540,9 @@ void FixRigid::set_v()
|
|||
v2 = v[i][2];
|
||||
}
|
||||
|
||||
v[i][0] = omega[ibody][1]*delta[2] - omega[ibody][2]*delta[1] +
|
||||
vcm[ibody][0];
|
||||
v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] +
|
||||
vcm[ibody][1];
|
||||
v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] +
|
||||
vcm[ibody][2];
|
||||
v[i][0] = omega[ibody][1]*delta[2] - omega[ibody][2]*delta[1] + vcm[ibody][0];
|
||||
v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] + vcm[ibody][1];
|
||||
v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] + vcm[ibody][2];
|
||||
|
||||
// virial = unwrapped coords dotted into body constraint force
|
||||
// body constraint force = implied force due to v change minus f external
|
||||
|
|
@ -1658,8 +1640,7 @@ void FixRigid::setup_bodies_static()
|
|||
{
|
||||
int i,ibody;
|
||||
|
||||
// extended = 1 if any particle in a rigid body is finite size
|
||||
// or has a dipole moment
|
||||
// extended = 1 if any particle in a rigid body is finite size or has a dipole moment
|
||||
|
||||
extended = orientflag = dorientflag = 0;
|
||||
|
||||
|
|
@ -1822,6 +1803,11 @@ void FixRigid::setup_bodies_static()
|
|||
|
||||
int *inbody;
|
||||
if (inpfile) {
|
||||
// must call it here so it doesn't override read in data but
|
||||
// initialize bodies whose dynamic settings not set in inpfile
|
||||
|
||||
setup_bodies_dynamic();
|
||||
|
||||
memory->create(inbody,nbody,"rigid:inbody");
|
||||
for (ibody = 0; ibody < nbody; ibody++) inbody[ibody] = 0;
|
||||
readfile(0,masstotal,xcm,vcm,angmom,imagebody,inbody);
|
||||
|
|
@ -2268,8 +2254,7 @@ void FixRigid::setup_bodies_dynamic()
|
|||
vxcm vycm vzcm lx ly lz ix iy iz
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRigid::readfile(int which, double *vec,
|
||||
double **array1, double **array2, double **array3,
|
||||
void FixRigid::readfile(int which, double *vec, double **array1, double **array2, double **array3,
|
||||
imageint *ivec, int *inbody)
|
||||
{
|
||||
int nchunk,id,eofflag,xbox,ybox,zbox;
|
||||
|
|
@ -2278,30 +2263,36 @@ void FixRigid::readfile(int which, double *vec,
|
|||
char *eof,*start,*next,*buf;
|
||||
char line[MAXLINE];
|
||||
|
||||
// open file and read and parse first non-empty, non-comment line containing the number of bodies
|
||||
if (me == 0) {
|
||||
fp = fopen(inpfile,"r");
|
||||
if (fp == nullptr)
|
||||
error->one(FLERR,"Cannot open fix rigid file {}: {}", inpfile,utils::getsyserror());
|
||||
error->one(FLERR,"Cannot open fix rigid infile {}: {}", inpfile, utils::getsyserror());
|
||||
while (true) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
if (eof == nullptr) error->one(FLERR,"Unexpected end of fix rigid file");
|
||||
if (eof == nullptr) error->one(FLERR,"Unexpected end of fix rigid infile");
|
||||
start = &line[strspn(line," \t\n\v\f\r")];
|
||||
if (*start != '\0' && *start != '#') break;
|
||||
}
|
||||
nlines = utils::inumeric(FLERR, utils::trim(line), true, lmp);
|
||||
if (which == 0)
|
||||
utils::logmesg(lmp, "Reading rigid body data for {} bodies from file {}\n", nlines, inpfile);
|
||||
if (nlines == 0) fclose(fp);
|
||||
}
|
||||
|
||||
MPI_Bcast(&nlines,1,MPI_INT,0,world);
|
||||
|
||||
// empty file with 0 lines is needed to trigger initial restart file generation
|
||||
if (nlines == 0) return; //error->all(FLERR,"Fix rigid file has no lines");
|
||||
// empty file with 0 lines is needed to trigger initial restart file
|
||||
// generation when no infile was previously used.
|
||||
|
||||
if (nlines == 0) return;
|
||||
else if (nlines < 0) error->all(FLERR,"Fix rigid infile has incorrect format");
|
||||
|
||||
char *buffer = new char[CHUNK*MAXLINE];
|
||||
int nread = 0;
|
||||
while (nread < nlines) {
|
||||
nchunk = MIN(nlines-nread,CHUNK);
|
||||
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
|
||||
if (eofflag) error->all(FLERR,"Unexpected end of fix rigid file");
|
||||
if (eofflag) error->all(FLERR,"Unexpected end of fix rigid infile");
|
||||
|
||||
buf = buffer;
|
||||
next = strchr(buf,'\n');
|
||||
|
|
@ -2328,7 +2319,7 @@ void FixRigid::readfile(int which, double *vec,
|
|||
id = values.next_int();
|
||||
if (rstyle == MOLECULE) {
|
||||
if (id <= 0 || id > maxmol)
|
||||
throw TokenizerException("invalid rigid body ID ", std::to_string(id));
|
||||
throw TokenizerException("invalid rigid molecule ID ", std::to_string(id));
|
||||
id = mol2body[id];
|
||||
} else id--;
|
||||
|
||||
|
|
@ -2365,7 +2356,7 @@ void FixRigid::readfile(int which, double *vec,
|
|||
array1[id][3] = values.next_double();
|
||||
}
|
||||
} catch (TokenizerException &e) {
|
||||
error->all(FLERR, "Invalid fix rigid file: {}", e.what());
|
||||
error->all(FLERR, "Invalid fix rigid infile: {}", e.what());
|
||||
}
|
||||
buf = next + 1;
|
||||
}
|
||||
|
|
@ -2384,7 +2375,7 @@ void FixRigid::readfile(int which, double *vec,
|
|||
|
||||
void FixRigid::write_restart_file(const char *file)
|
||||
{
|
||||
if (me) return;
|
||||
if (comm->me) return;
|
||||
|
||||
auto outfile = std::string(file) + ".rigid";
|
||||
FILE *fp = fopen(outfile.c_str(),"w");
|
||||
|
|
@ -2414,14 +2405,11 @@ void FixRigid::write_restart_file(const char *file)
|
|||
ybox = (imagebody[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (imagebody[i] >> IMG2BITS) - IMGMAX;
|
||||
|
||||
fprintf(fp,"%d %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g "
|
||||
"%.16g %.16g %.16g %.16g %.16g %.16g %d %d %d\n",
|
||||
id,masstotal[i],xcm[i][0],xcm[i][1],xcm[i][2],
|
||||
ispace[0][0],ispace[1][1],ispace[2][2],
|
||||
ispace[0][1],ispace[0][2],ispace[1][2],
|
||||
vcm[i][0],vcm[i][1],vcm[i][2],
|
||||
angmom[i][0],angmom[i][1],angmom[i][2],
|
||||
xbox,ybox,zbox);
|
||||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
|
||||
"%-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
|
||||
id,masstotal[i],xcm[i][0],xcm[i][1],xcm[i][2],ispace[0][0],ispace[1][1],ispace[2][2],
|
||||
ispace[0][1],ispace[0][2],ispace[1][2],vcm[i][0],vcm[i][1],vcm[i][2],
|
||||
angmom[i][0],angmom[i][1],angmom[i][2],xbox,ybox,zbox);
|
||||
}
|
||||
|
||||
fclose(fp);
|
||||
|
|
@ -2483,6 +2471,7 @@ void FixRigid::copy_arrays(int i, int j, int /*delflag*/)
|
|||
displace[j][0] = displace[i][0];
|
||||
displace[j][1] = displace[i][1];
|
||||
displace[j][2] = displace[i][2];
|
||||
|
||||
if (extended) {
|
||||
eflags[j] = eflags[i];
|
||||
for (int k = 0; k < orientflag; k++)
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "random_mars.h"
|
||||
#include "respa.h"
|
||||
#include "rigid_const.h"
|
||||
#include "tokenizer.h"
|
||||
#include "update.h"
|
||||
#include "variable.h"
|
||||
|
||||
|
|
@ -116,11 +117,9 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
|
|||
int is_double,cols;
|
||||
int custom_index = atom->find_custom(arg[4]+2,is_double,cols);
|
||||
if (custom_index == -1)
|
||||
error->all(FLERR,"Fix rigid/small custom requires "
|
||||
"previously defined property/atom");
|
||||
error->all(FLERR,"Fix rigid/small custom requires previously defined property/atom");
|
||||
else if (is_double || cols)
|
||||
error->all(FLERR,"Fix rigid/small custom requires "
|
||||
"integer-valued property/atom vector");
|
||||
error->all(FLERR,"Fix rigid/small custom requires integer-valued property/atom vector");
|
||||
int minval = INT_MAX;
|
||||
int *value = atom->ivector[custom_index];
|
||||
for (i = 0; i < nlocal; i++)
|
||||
|
|
@ -136,11 +135,10 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
|
|||
} else if (utils::strmatch(arg[4],"^v_")) {
|
||||
int ivariable = input->variable->find(arg[4]+2);
|
||||
if (ivariable < 0)
|
||||
error->all(FLERR,"Variable name for fix rigid/small custom "
|
||||
"does not exist");
|
||||
error->all(FLERR,"Variable {} for fix rigid/small custom does not exist", arg[4]+2);
|
||||
if (input->variable->atomstyle(ivariable) == 0)
|
||||
error->all(FLERR,"Fix rigid/small custom variable is not "
|
||||
"atom-style variable");
|
||||
error->all(FLERR,"Fix rigid/small custom variable {} is not atom-style variable",
|
||||
arg[4]+2);
|
||||
double *value = new double[nlocal];
|
||||
input->variable->compute_atom(ivariable,0,value,1,0);
|
||||
int minval = INT_MAX;
|
||||
|
|
@ -398,8 +396,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (customflag) delete[] bodyID;
|
||||
|
||||
if (comm->me == 0)
|
||||
utils::logmesg(lmp," create bodies CPU = {:.3f} seconds\n",
|
||||
platform::walltime()-time1);
|
||||
utils::logmesg(lmp," create bodies CPU = {:.3f} seconds\n", platform::walltime()-time1);
|
||||
|
||||
// set nlocal_body and allocate bodies I own
|
||||
|
||||
|
|
@ -411,8 +408,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
nmax_body = 0;
|
||||
while (nmax_body < nlocal_body) nmax_body += DELTA_BODY;
|
||||
body = (Body *) memory->smalloc(nmax_body*sizeof(Body),
|
||||
"rigid/small:body");
|
||||
body = (Body *) memory->smalloc(nmax_body*sizeof(Body), "rigid/small:body");
|
||||
|
||||
// set bodyown for owned atoms
|
||||
|
||||
|
|
@ -527,26 +523,22 @@ int FixRigidSmall::setmask()
|
|||
|
||||
void FixRigidSmall::init()
|
||||
{
|
||||
int i;
|
||||
|
||||
triclinic = domain->triclinic;
|
||||
|
||||
// warn if more than one rigid fix
|
||||
// if earlyflag, warn if any post-force fixes come after a rigid fix
|
||||
|
||||
int count = 0;
|
||||
for (i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->rigid_flag) count++;
|
||||
for (auto ifix : modify->get_fix_list())
|
||||
if (ifix->rigid_flag) count++;
|
||||
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
|
||||
|
||||
if (earlyflag) {
|
||||
int rflag = 0;
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (modify->fix[i]->rigid_flag) rflag = 1;
|
||||
if (rflag && (modify->fmask[i] & POST_FORCE) &&
|
||||
!modify->fix[i]->rigid_flag)
|
||||
error->warning(FLERR,"Fix {} alters forces after fix rigid",
|
||||
modify->fix[i]->id);
|
||||
bool rflag = false;
|
||||
for (auto ifix : modify->get_fix_list()) {
|
||||
if (ifix->rigid_flag) rflag = true;
|
||||
if ((comm->me == 0) && rflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
|
||||
error->warning(FLERR,"Fix {} alters forces after fix rigid", ifix->id);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -556,36 +548,30 @@ void FixRigidSmall::init()
|
|||
// and gravity is not applied correctly
|
||||
|
||||
if ((inpfile || onemols) && !id_gravity) {
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (strcmp(modify->fix[i]->style,"gravity") == 0) {
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Gravity may not be correctly applied "
|
||||
"to rigid bodies if they consist of "
|
||||
"overlapped particles");
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (modify->get_fix_by_style("^gravity").size() > 0)
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Gravity may not be correctly applied to rigid "
|
||||
"bodies if they consist of overlapped particles");
|
||||
}
|
||||
|
||||
// error if a fix changing the box comes before rigid fix
|
||||
|
||||
for (i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->box_change) break;
|
||||
if (i < modify->nfix) {
|
||||
for (int j = i+1; j < modify->nfix; j++)
|
||||
if (utils::strmatch(modify->fix[j]->style,"^rigid"))
|
||||
bool boxflag = false;
|
||||
for (auto ifix : modify->get_fix_list()) {
|
||||
if (ifix->box_change) boxflag = true;
|
||||
if (boxflag && utils::strmatch(ifix->style,"^rigid"))
|
||||
error->all(FLERR,"Rigid fixes must come before any box changing fix");
|
||||
}
|
||||
|
||||
// add gravity forces based on gravity vector from fix
|
||||
|
||||
if (id_gravity) {
|
||||
int ifix = modify->find_fix(id_gravity);
|
||||
if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");
|
||||
if (!utils::strmatch(modify->fix[ifix]->style,"^gravity"))
|
||||
error->all(FLERR,"Fix rigid gravity fix ID is not a gravity fix style");
|
||||
auto ifix = modify->get_fix_by_id(id_gravity);
|
||||
if (!ifix) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID {}", id_gravity);
|
||||
if (!utils::strmatch(ifix->style,"^gravity"))
|
||||
error->all(FLERR,"Fix rigid/small gravity fix ID {} is not a gravity fix style", id_gravity);
|
||||
int tmp;
|
||||
gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
|
||||
gvec = (double *) ifix->extract("gvec", tmp);
|
||||
}
|
||||
|
||||
// timestep info
|
||||
|
|
@ -1995,6 +1981,11 @@ void FixRigidSmall::setup_bodies_static()
|
|||
|
||||
int *inbody;
|
||||
if (inpfile) {
|
||||
// must call it here so it doesn't override read in data but
|
||||
// initialize bodies whose dynamic settings not set in inpfile
|
||||
|
||||
setup_bodies_dynamic();
|
||||
|
||||
memory->create(inbody,nlocal_body,"rigid/small:inbody");
|
||||
for (ibody = 0; ibody < nlocal_body; ibody++) inbody[ibody] = 0;
|
||||
readfile(0,nullptr,inbody);
|
||||
|
|
@ -2467,8 +2458,7 @@ void FixRigidSmall::setup_bodies_dynamic()
|
|||
|
||||
void FixRigidSmall::readfile(int which, double **array, int *inbody)
|
||||
{
|
||||
int i,j,m,nchunk,eofflag,nlines,xbox,ybox,zbox;
|
||||
tagint id;
|
||||
int nchunk,eofflag,nlines,xbox,ybox,zbox;
|
||||
FILE *fp;
|
||||
char *eof,*start,*next,*buf;
|
||||
char line[MAXLINE];
|
||||
|
|
@ -2480,7 +2470,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
|
|||
int nlocal = atom->nlocal;
|
||||
|
||||
std::map<tagint,int> hash;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (bodyown[i] >= 0) hash[atom->molecule[i]] = bodyown[i];
|
||||
|
||||
// open file and read header
|
||||
|
|
@ -2488,24 +2478,27 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
|
|||
if (me == 0) {
|
||||
fp = fopen(inpfile,"r");
|
||||
if (fp == nullptr)
|
||||
error->one(FLERR,"Cannot open fix rigid/small file {}: {}",
|
||||
inpfile,utils::getsyserror());
|
||||
error->one(FLERR,"Cannot open fix rigid/small file {}: {}", inpfile, utils::getsyserror());
|
||||
while (true) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
if (eof == nullptr)
|
||||
error->one(FLERR,"Unexpected end of fix rigid/small file");
|
||||
if (eof == nullptr) error->one(FLERR,"Unexpected end of fix rigid/small file");
|
||||
start = &line[strspn(line," \t\n\v\f\r")];
|
||||
if (*start != '\0' && *start != '#') break;
|
||||
}
|
||||
|
||||
sscanf(line,"%d",&nlines);
|
||||
nlines = utils::inumeric(FLERR, utils::trim(line), true, lmp);
|
||||
if (which == 0)
|
||||
utils::logmesg(lmp, "Reading rigid body data for {} bodies from file {}\n", nlines, inpfile);
|
||||
if (nlines == 0) fclose(fp);
|
||||
}
|
||||
|
||||
MPI_Bcast(&nlines,1,MPI_INT,0,world);
|
||||
|
||||
char *buffer = new char[CHUNK*MAXLINE];
|
||||
char **values = new char*[ATTRIBUTE_PERBODY];
|
||||
// empty file with 0 lines is needed to trigger initial restart file
|
||||
// generation when no infile was previously used.
|
||||
|
||||
if (nlines == 0) return;
|
||||
else if (nlines < 0) error->all(FLERR,"Fix rigid infile has incorrect format");
|
||||
|
||||
char *buffer = new char[CHUNK*MAXLINE];
|
||||
int nread = 0;
|
||||
while (nread < nlines) {
|
||||
nchunk = MIN(nlines-nread,CHUNK);
|
||||
|
|
@ -2515,7 +2508,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
|
|||
buf = buffer;
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
int nwords = utils::trim_and_count_words(buf);
|
||||
int nwords = utils::count_words(utils::trim_comment(buf));
|
||||
*next = '\n';
|
||||
|
||||
if (nwords != ATTRIBUTE_PERBODY)
|
||||
|
|
@ -2527,59 +2520,61 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
|
|||
// for which = 0, store all but inertia directly in body struct
|
||||
// for which = 1, store inertia tensor array, invert 3,4,5 values to Voigt
|
||||
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
for (int i = 0; i < nchunk; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
|
||||
values[0] = strtok(buf," \t\n\r\f");
|
||||
for (j = 1; j < nwords; j++)
|
||||
values[j] = strtok(nullptr," \t\n\r\f");
|
||||
try {
|
||||
ValueTokenizer values(buf);
|
||||
tagint id = values.next_tagint();
|
||||
|
||||
id = ATOTAGINT(values[0]);
|
||||
if (id <= 0 || id > maxmol)
|
||||
error->all(FLERR,"Invalid rigid body ID in fix rigid/small file");
|
||||
if (hash.find(id) == hash.end()) {
|
||||
buf = next + 1;
|
||||
continue;
|
||||
if (id <= 0 || id > maxmol)
|
||||
error->all(FLERR,"Invalid rigid body molecude ID {} in fix rigid/small file", id);
|
||||
|
||||
if (hash.find(id) == hash.end()) {
|
||||
buf = next + 1;
|
||||
continue;
|
||||
}
|
||||
int m = hash[id];
|
||||
inbody[m] = 1;
|
||||
|
||||
if (which == 0) {
|
||||
body[m].mass = values.next_double();
|
||||
body[m].xcm[0] = values.next_double();
|
||||
body[m].xcm[1] = values.next_double();
|
||||
body[m].xcm[2] = values.next_double();
|
||||
values.skip(6);
|
||||
body[m].vcm[0] = values.next_double();
|
||||
body[m].vcm[1] = values.next_double();
|
||||
body[m].vcm[2] = values.next_double();
|
||||
body[m].angmom[0] = values.next_double();
|
||||
body[m].angmom[1] = values.next_double();
|
||||
body[m].angmom[2] = values.next_double();
|
||||
xbox = values.next_int();
|
||||
ybox = values.next_int();
|
||||
zbox = values.next_int();
|
||||
body[m].image = ((imageint) (xbox + IMGMAX) & IMGMASK) |
|
||||
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
|
||||
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
|
||||
} else {
|
||||
values.skip(4);
|
||||
array[m][0] = values.next_double();
|
||||
array[m][1] = values.next_double();
|
||||
array[m][2] = values.next_double();
|
||||
array[m][5] = values.next_double();
|
||||
array[m][4] = values.next_double();
|
||||
array[m][3] = values.next_double();
|
||||
}
|
||||
} catch (TokenizerException &e) {
|
||||
error->all(FLERR, "Invalid fix rigid/small infile: {}", e.what());
|
||||
}
|
||||
m = hash[id];
|
||||
inbody[m] = 1;
|
||||
|
||||
if (which == 0) {
|
||||
body[m].mass = atof(values[1]);
|
||||
body[m].xcm[0] = atof(values[2]);
|
||||
body[m].xcm[1] = atof(values[3]);
|
||||
body[m].xcm[2] = atof(values[4]);
|
||||
body[m].vcm[0] = atof(values[11]);
|
||||
body[m].vcm[1] = atof(values[12]);
|
||||
body[m].vcm[2] = atof(values[13]);
|
||||
body[m].angmom[0] = atof(values[14]);
|
||||
body[m].angmom[1] = atof(values[15]);
|
||||
body[m].angmom[2] = atof(values[16]);
|
||||
xbox = atoi(values[17]);
|
||||
ybox = atoi(values[18]);
|
||||
zbox = atoi(values[19]);
|
||||
body[m].image = ((imageint) (xbox + IMGMAX) & IMGMASK) |
|
||||
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
|
||||
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
|
||||
} else {
|
||||
array[m][0] = atof(values[5]);
|
||||
array[m][1] = atof(values[6]);
|
||||
array[m][2] = atof(values[7]);
|
||||
array[m][3] = atof(values[10]);
|
||||
array[m][4] = atof(values[9]);
|
||||
array[m][5] = atof(values[8]);
|
||||
}
|
||||
|
||||
buf = next + 1;
|
||||
}
|
||||
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
if (me == 0) fclose(fp);
|
||||
|
||||
delete[] buffer;
|
||||
delete[] values;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
Loading…
Reference in New Issue