add input examples for custom rigid body definition
This commit is contained in:
Axel Kohlmeyer
83
examples/rigid/bodies.txt
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83
examples/rigid/bodies.txt
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81
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1 1
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2 1
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3 1
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4 1
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5 1
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6 1
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7 1
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8 1
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9 1
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10 2
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11 2
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12 2
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13 2
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14 2
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15 2
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16 2
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17 2
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18 2
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19 3
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20 3
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21 3
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22 3
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23 3
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24 3
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25 3
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26 3
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27 3
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28 4
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29 4
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30 4
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31 4
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32 4
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33 4
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34 4
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35 4
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36 4
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37 5
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38 5
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39 5
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40 5
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41 5
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42 5
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43 5
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44 5
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45 5
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46 6
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47 6
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48 6
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49 6
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50 6
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51 6
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52 6
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53 6
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54 6
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55 7
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56 7
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57 7
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58 7
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59 7
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60 7
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61 7
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62 7
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63 7
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64 8
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65 8
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66 8
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67 8
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68 8
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69 8
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70 8
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71 8
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72 8
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73 9
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74 9
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75 9
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76 9
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77 9
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78 9
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79 9
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80 9
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81 9
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185
examples/rigid/data.rigid-property
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185
examples/rigid/data.rigid-property
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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 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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Bodies
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1 1
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2 1
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3 1
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4 1
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5 1
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6 1
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7 1
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8 1
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9 1
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10 2
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11 2
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12 2
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13 2
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14 2
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15 2
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16 2
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17 2
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18 2
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19 3
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20 3
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21 3
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22 3
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23 3
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24 3
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25 3
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26 3
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27 3
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28 4
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29 4
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30 4
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31 4
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32 4
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33 4
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34 4
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35 4
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36 4
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37 5
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38 5
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39 5
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40 5
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41 5
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42 5
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43 5
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44 5
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45 5
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46 6
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47 6
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48 6
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49 6
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50 6
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51 6
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52 6
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53 6
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54 6
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55 7
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56 7
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57 7
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58 7
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59 7
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60 7
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61 7
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62 7
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63 7
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64 8
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65 8
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66 8
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67 8
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68 8
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69 8
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70 8
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71 8
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72 8
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73 9
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74 9
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75 9
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76 9
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77 9
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78 9
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79 9
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80 9
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81 9
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83
examples/rigid/in.rigid-atomfile
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83
examples/rigid/in.rigid-atomfile
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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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atom_modify map array
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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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variable bodies atomfile bodies.txt
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fix 1 all rigid custom v_bodies
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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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#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
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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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#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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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 &
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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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83
examples/rigid/in.rigid-atomvar
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83
examples/rigid/in.rigid-atomvar
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@ -0,0 +1,83 @@
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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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atom_modify map array
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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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variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
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fix 1 all rigid custom v_bodies
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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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#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
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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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#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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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 &
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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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85
examples/rigid/in.rigid-property
Normal file
85
examples/rigid/in.rigid-property
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@ -0,0 +1,85 @@
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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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atom_modify map array
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pair_style lj/cut 2.5
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fix 0 all property/atom i_bodies
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read_data data.rigid-property fix 0 NULL Bodies
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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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# assemble bodies from per-atom custom integer property bodies
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fix 1 all rigid custom i_bodies
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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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#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
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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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#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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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 &
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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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