add example for Python with vector-style variable
This commit is contained in:
Steve Plimpton
234
examples/python/dump.1May25.python.wrap.g++.1
Normal file
234
examples/python/dump.1May25.python.wrap.g++.1
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ITEM: TIMESTEP
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0
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ITEM: NUMBER OF ATOMS
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108
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ITEM: BOX BOUNDS pp pp pp
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0.0000000000000000e+00 5.0387885741475218e+00
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0.0000000000000000e+00 5.0387885741475218e+00
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0.0000000000000000e+00 5.0387885741475218e+00
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ITEM: ATOMS id x y z v_xtrunc v_ytrunc v_ztrunc
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1 0 0 0 0 0 0
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2 0.839798 0.839798 0 0 0 0
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3 0.839798 0 0.839798 0 0 0
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4 0 0.839798 0.839798 0 0 0
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5 1.6796 0 0 1 0 0
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6 2.51939 0.839798 0 2 0 0
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7 2.51939 0 0.839798 2 0 0
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8 1.6796 0.839798 0.839798 1 0 0
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9 3.35919 0 0 3 0 0
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10 4.19899 0.839798 0 4 0 0
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11 4.19899 0 0.839798 4 0 0
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12 3.35919 0.839798 0.839798 3 0 0
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13 0 1.6796 0 0 1 0
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14 0.839798 2.51939 0 0 2 0
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15 0.839798 1.6796 0.839798 0 1 0
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16 0 2.51939 0.839798 0 2 0
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17 1.6796 1.6796 0 1 1 0
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18 2.51939 2.51939 0 2 2 0
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19 2.51939 1.6796 0.839798 2 1 0
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20 1.6796 2.51939 0.839798 1 2 0
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21 3.35919 1.6796 0 3 1 0
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22 4.19899 2.51939 0 4 2 0
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23 4.19899 1.6796 0.839798 4 1 0
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24 3.35919 2.51939 0.839798 3 2 0
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25 0 3.35919 0 0 3 0
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26 0.839798 4.19899 0 0 4 0
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27 0.839798 3.35919 0.839798 0 3 0
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28 0 4.19899 0.839798 0 4 0
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29 1.6796 3.35919 0 1 3 0
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30 2.51939 4.19899 0 2 4 0
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31 2.51939 3.35919 0.839798 2 3 0
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32 1.6796 4.19899 0.839798 1 4 0
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33 3.35919 3.35919 0 3 3 0
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34 4.19899 4.19899 0 4 4 0
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35 4.19899 3.35919 0.839798 4 3 0
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36 3.35919 4.19899 0.839798 3 4 0
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37 0 0 1.6796 0 0 1
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38 0.839798 0.839798 1.6796 0 0 1
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39 0.839798 0 2.51939 0 0 2
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40 0 0.839798 2.51939 0 0 2
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41 1.6796 0 1.6796 1 0 1
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42 2.51939 0.839798 1.6796 2 0 1
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43 2.51939 0 2.51939 2 0 2
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44 1.6796 0.839798 2.51939 1 0 2
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45 3.35919 0 1.6796 3 0 1
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46 4.19899 0.839798 1.6796 4 0 1
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47 4.19899 0 2.51939 4 0 2
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48 3.35919 0.839798 2.51939 3 0 2
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49 0 1.6796 1.6796 0 1 1
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50 0.839798 2.51939 1.6796 0 2 1
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51 0.839798 1.6796 2.51939 0 1 2
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52 0 2.51939 2.51939 0 2 2
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53 1.6796 1.6796 1.6796 1 1 1
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54 2.51939 2.51939 1.6796 2 2 1
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55 2.51939 1.6796 2.51939 2 1 2
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56 1.6796 2.51939 2.51939 1 2 2
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57 3.35919 1.6796 1.6796 3 1 1
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58 4.19899 2.51939 1.6796 4 2 1
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59 4.19899 1.6796 2.51939 4 1 2
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60 3.35919 2.51939 2.51939 3 2 2
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61 0 3.35919 1.6796 0 3 1
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62 0.839798 4.19899 1.6796 0 4 1
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63 0.839798 3.35919 2.51939 0 3 2
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64 0 4.19899 2.51939 0 4 2
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65 1.6796 3.35919 1.6796 1 3 1
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66 2.51939 4.19899 1.6796 2 4 1
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67 2.51939 3.35919 2.51939 2 3 2
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68 1.6796 4.19899 2.51939 1 4 2
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69 3.35919 3.35919 1.6796 3 3 1
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70 4.19899 4.19899 1.6796 4 4 1
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71 4.19899 3.35919 2.51939 4 3 2
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72 3.35919 4.19899 2.51939 3 4 2
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73 0 0 3.35919 0 0 3
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74 0.839798 0.839798 3.35919 0 0 3
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75 0.839798 0 4.19899 0 0 4
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76 0 0.839798 4.19899 0 0 4
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77 1.6796 0 3.35919 1 0 3
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78 2.51939 0.839798 3.35919 2 0 3
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79 2.51939 0 4.19899 2 0 4
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80 1.6796 0.839798 4.19899 1 0 4
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81 3.35919 0 3.35919 3 0 3
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82 4.19899 0.839798 3.35919 4 0 3
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83 4.19899 0 4.19899 4 0 4
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84 3.35919 0.839798 4.19899 3 0 4
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85 0 1.6796 3.35919 0 1 3
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86 0.839798 2.51939 3.35919 0 2 3
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87 0.839798 1.6796 4.19899 0 1 4
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88 0 2.51939 4.19899 0 2 4
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89 1.6796 1.6796 3.35919 1 1 3
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90 2.51939 2.51939 3.35919 2 2 3
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91 2.51939 1.6796 4.19899 2 1 4
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92 1.6796 2.51939 4.19899 1 2 4
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93 3.35919 1.6796 3.35919 3 1 3
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94 4.19899 2.51939 3.35919 4 2 3
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95 4.19899 1.6796 4.19899 4 1 4
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96 3.35919 2.51939 4.19899 3 2 4
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97 0 3.35919 3.35919 0 3 3
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98 0.839798 4.19899 3.35919 0 4 3
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99 0.839798 3.35919 4.19899 0 3 4
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100 0 4.19899 4.19899 0 4 4
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101 1.6796 3.35919 3.35919 1 3 3
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102 2.51939 4.19899 3.35919 2 4 3
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103 2.51939 3.35919 4.19899 2 3 4
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104 1.6796 4.19899 4.19899 1 4 4
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105 3.35919 3.35919 3.35919 3 3 3
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106 4.19899 4.19899 3.35919 4 4 3
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107 4.19899 3.35919 4.19899 4 3 4
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108 3.35919 4.19899 4.19899 3 4 4
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ITEM: TIMESTEP
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100
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ITEM: NUMBER OF ATOMS
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108
|
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ITEM: BOX BOUNDS pp pp pp
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0.0000000000000000e+00 5.0387885741475218e+00
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0.0000000000000000e+00 5.0387885741475218e+00
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0.0000000000000000e+00 5.0387885741475218e+00
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ITEM: ATOMS id x y z v_xtrunc v_ytrunc v_ztrunc
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1 4.97801 0.0605812 4.88474 4 0 4
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2 0.800305 0.813213 0.0576603 0 0 0
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3 0.6485 5.00484 0.836947 0 5 0
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4 5.01236 0.786108 0.77507 5 0 0
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5 1.50261 4.9277 4.9755 1 4 4
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6 2.46756 0.653742 5.0003 2 0 5
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7 2.55699 4.96491 0.926671 2 4 0
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8 1.62464 0.676882 0.777822 1 0 0
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9 3.57018 0.00324557 4.76943 3 0 4
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10 4.24909 0.985667 5.01613 4 0 5
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11 4.13124 0.178555 0.700886 4 0 0
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12 3.22537 0.963341 0.639686 3 0 0
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13 4.90815 1.75715 0.0826318 4 1 0
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14 1.00239 2.45421 0.0111309 1 2 0
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15 0.88902 1.62097 0.874547 0 1 0
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16 0.269512 2.41383 0.844638 0 2 0
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17 1.54513 1.51174 0.0869798 1 1 0
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18 2.0637 2.5991 0.0826392 2 2 0
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19 2.44634 1.71869 0.918144 2 1 0
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20 1.57997 2.52559 1.04361 1 2 1
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21 3.26063 2.10027 0.0160498 3 2 0
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22 4.21774 2.61172 0.0367453 4 2 0
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23 4.32215 1.8333 0.925663 4 1 0
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24 3.38151 2.6788 0.906258 3 2 0
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25 0.275459 3.26838 0.21932 0 3 0
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26 0.675354 4.14887 4.94054 0 4 4
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27 0.867201 3.35405 1.17655 0 3 1
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28 4.78788 4.34273 0.478103 4 4 0
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29 1.42014 3.50181 0.191388 1 3 0
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30 2.39935 4.14279 0.0726977 2 4 0
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31 2.68157 3.57418 0.921633 2 3 0
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32 1.77965 4.13041 0.925765 1 4 0
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33 3.10555 3.22911 5.00703 3 3 5
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34 4.24908 3.67507 4.83053 4 3 4
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35 4.2444 3.59428 0.837193 4 3 0
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36 3.52155 4.21032 0.423884 3 4 0
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37 0.00881412 4.90616 1.74242 0 4 1
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38 0.800033 0.812556 1.72553 0 0 1
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39 0.929754 0.0251285 2.53734 0 0 2
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40 0.0189933 0.897729 2.4272 0 0 2
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41 1.77025 0.0864618 1.69637 1 0 1
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42 2.6077 0.984882 1.7897 2 0 1
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43 2.55819 4.95626 2.45373 2 4 2
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44 1.77963 0.875522 2.5056 1 0 2
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45 3.50499 0.0189748 1.5186 3 0 1
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46 4.47856 0.849521 1.59138 4 0 1
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47 3.99 0.309367 2.42507 3 0 2
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48 3.06373 0.748905 2.87477 3 0 2
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49 0.149175 1.72252 1.81302 0 1 1
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50 0.963279 2.42412 1.76899 0 2 1
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51 0.879984 1.74899 2.55389 0 1 2
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52 0.211736 2.57456 2.48446 0 2 2
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53 1.75238 1.7433 1.79028 1 1 1
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54 2.61023 2.6802 1.55816 2 2 1
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55 2.55259 1.72904 2.60295 2 1 2
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56 1.7903 2.56204 2.41895 1 2 2
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57 3.43857 1.71819 1.54054 3 1 1
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58 4.20455 2.5331 1.87607 4 2 1
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59 4.12961 1.48438 2.40107 4 1 2
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60 3.36606 2.52455 2.67203 3 2 2
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61 0.0138563 3.23504 1.76147 0 3 1
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62 0.968224 4.42746 1.67526 0 4 1
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63 0.965745 3.43479 2.52674 0 3 2
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64 0.144542 4.27264 2.61793 0 4 2
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65 1.7741 3.32184 1.66819 1 3 1
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66 2.4878 4.29352 1.69069 2 4 1
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67 2.56992 3.44579 2.4534 2 3 2
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68 1.72356 4.2344 2.49376 1 4 2
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69 3.43363 3.36417 1.87451 3 3 1
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70 4.32623 4.1046 1.69102 4 4 1
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71 4.22927 3.23505 2.64208 4 3 2
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72 3.41086 4.28362 2.42553 3 4 2
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73 4.85349 0.0953155 3.14546 4 0 3
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74 0.833593 0.840282 3.27238 0 0 3
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75 0.578712 4.99093 3.85234 0 4 3
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76 0.119704 1.00404 4.09942 0 1 4
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77 1.78347 4.95586 3.31184 1 4 3
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78 2.34318 0.736887 3.54475 2 0 3
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79 2.34858 4.82316 4.28272 2 4 4
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80 1.55893 0.765128 4.31112 1 0 4
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81 3.13128 0.0257347 3.70936 3 0 3
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82 4.10851 0.877375 3.36388 4 0 3
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83 4.30691 4.69041 4.14081 4 4 4
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84 3.48471 1.07347 4.35888 3 1 4
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85 0.0668209 1.77975 3.29313 0 1 3
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86 0.894798 2.5043 3.34172 0 2 3
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87 0.743432 1.71961 4.3483 0 1 4
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88 0.135168 2.69084 4.12098 0 2 4
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89 1.73749 1.5259 3.46692 1 1 3
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90 2.47391 2.57508 3.27574 2 2 3
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91 2.4825 1.46064 4.38907 2 1 4
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92 1.67786 2.47309 4.03082 1 2 4
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93 3.34694 1.70248 3.44784 3 1 3
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94 4.20676 2.29697 3.23228 4 2 3
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95 4.31748 1.76411 4.20898 4 1 4
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96 3.1135 2.59262 4.08996 3 2 4
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97 0.0727406 3.44797 3.30247 0 3 3
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98 1.0752 4.05296 3.38036 1 4 3
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99 1.0085 3.35058 4.3598 1 3 4
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100 0.054939 4.00087 4.11831 0 4 4
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101 1.72259 3.24691 3.19685 1 3 3
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102 2.54324 4.21582 3.29642 2 4 3
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103 2.33008 3.38603 4.27885 2 3 4
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104 1.65617 4.10852 4.3491 1 4 4
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105 3.14646 3.43756 3.28105 3 3 3
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106 4.09781 4.10691 3.24439 4 4 3
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107 4.1529 3.22538 3.79605 4 3 3
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108 3.16394 3.96553 4.31023 3 3 4
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234
examples/python/dump.1May25.python.wrap.g++.4
Normal file
234
examples/python/dump.1May25.python.wrap.g++.4
Normal file
@ -0,0 +1,234 @@
|
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ITEM: TIMESTEP
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0
|
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ITEM: NUMBER OF ATOMS
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108
|
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ITEM: BOX BOUNDS pp pp pp
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0.0000000000000000e+00 5.0387885741475218e+00
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0.0000000000000000e+00 5.0387885741475218e+00
|
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0.0000000000000000e+00 5.0387885741475218e+00
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ITEM: ATOMS id x y z v_xtrunc v_ytrunc v_ztrunc
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1 0 0 0 0 0 0
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2 0.839798 0.839798 0 0 0 0
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3 0.839798 0 0.839798 0 0 0
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4 0 0.839798 0.839798 0 0 0
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13 0 1.6796 0 0 1 0
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14 0.839798 1.6796 0.839798 0 1 0
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19 0 0 1.6796 0 0 1
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20 0.839798 0.839798 1.6796 0 0 1
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25 0 1.6796 1.6796 0 1 1
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5 1.6796 0 0 1 0 0
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6 2.51939 0.839798 0 2 0 0
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7 2.51939 0 0.839798 2 0 0
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8 1.6796 0.839798 0.839798 1 0 0
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15 1.6796 1.6796 0 1 1 0
|
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16 2.51939 1.6796 0.839798 2 1 0
|
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21 1.6796 0 1.6796 1 0 1
|
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22 2.51939 0.839798 1.6796 2 0 1
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26 1.6796 1.6796 1.6796 1 1 1
|
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9 3.35919 0 0 3 0 0
|
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10 4.19899 0.839798 0 4 0 0
|
||||
11 4.19899 0 0.839798 4 0 0
|
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12 3.35919 0.839798 0.839798 3 0 0
|
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17 3.35919 1.6796 0 3 1 0
|
||||
18 4.19899 1.6796 0.839798 4 1 0
|
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23 3.35919 0 1.6796 3 0 1
|
||||
24 4.19899 0.839798 1.6796 4 0 1
|
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27 3.35919 1.6796 1.6796 3 1 1
|
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28 0.839798 0 2.51939 0 0 2
|
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29 0 0.839798 2.51939 0 0 2
|
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34 0.839798 1.6796 2.51939 0 1 2
|
||||
37 0 0 3.35919 0 0 3
|
||||
38 0.839798 0.839798 3.35919 0 0 3
|
||||
39 0.839798 0 4.19899 0 0 4
|
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40 0 0.839798 4.19899 0 0 4
|
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49 0 1.6796 3.35919 0 1 3
|
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50 0.839798 1.6796 4.19899 0 1 4
|
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30 2.51939 0 2.51939 2 0 2
|
||||
31 1.6796 0.839798 2.51939 1 0 2
|
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35 2.51939 1.6796 2.51939 2 1 2
|
||||
41 1.6796 0 3.35919 1 0 3
|
||||
42 2.51939 0.839798 3.35919 2 0 3
|
||||
43 2.51939 0 4.19899 2 0 4
|
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44 1.6796 0.839798 4.19899 1 0 4
|
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51 1.6796 1.6796 3.35919 1 1 3
|
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52 2.51939 1.6796 4.19899 2 1 4
|
||||
32 4.19899 0 2.51939 4 0 2
|
||||
33 3.35919 0.839798 2.51939 3 0 2
|
||||
36 4.19899 1.6796 2.51939 4 1 2
|
||||
45 3.35919 0 3.35919 3 0 3
|
||||
46 4.19899 0.839798 3.35919 4 0 3
|
||||
47 4.19899 0 4.19899 4 0 4
|
||||
48 3.35919 0.839798 4.19899 3 0 4
|
||||
53 3.35919 1.6796 3.35919 3 1 3
|
||||
54 4.19899 1.6796 4.19899 4 1 4
|
||||
55 0.839798 2.51939 0 0 2 0
|
||||
56 0 2.51939 0.839798 0 2 0
|
||||
61 0 3.35919 0 0 3 0
|
||||
62 0.839798 4.19899 0 0 4 0
|
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63 0.839798 3.35919 0.839798 0 3 0
|
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64 0 4.19899 0.839798 0 4 0
|
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73 0.839798 2.51939 1.6796 0 2 1
|
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76 0 3.35919 1.6796 0 3 1
|
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77 0.839798 4.19899 1.6796 0 4 1
|
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57 2.51939 2.51939 0 2 2 0
|
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58 1.6796 2.51939 0.839798 1 2 0
|
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65 1.6796 3.35919 0 1 3 0
|
||||
66 2.51939 4.19899 0 2 4 0
|
||||
67 2.51939 3.35919 0.839798 2 3 0
|
||||
68 1.6796 4.19899 0.839798 1 4 0
|
||||
74 2.51939 2.51939 1.6796 2 2 1
|
||||
78 1.6796 3.35919 1.6796 1 3 1
|
||||
79 2.51939 4.19899 1.6796 2 4 1
|
||||
59 4.19899 2.51939 0 4 2 0
|
||||
60 3.35919 2.51939 0.839798 3 2 0
|
||||
69 3.35919 3.35919 0 3 3 0
|
||||
70 4.19899 4.19899 0 4 4 0
|
||||
71 4.19899 3.35919 0.839798 4 3 0
|
||||
72 3.35919 4.19899 0.839798 3 4 0
|
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75 4.19899 2.51939 1.6796 4 2 1
|
||||
80 3.35919 3.35919 1.6796 3 3 1
|
||||
81 4.19899 4.19899 1.6796 4 4 1
|
||||
82 0 2.51939 2.51939 0 2 2
|
||||
85 0.839798 3.35919 2.51939 0 3 2
|
||||
86 0 4.19899 2.51939 0 4 2
|
||||
91 0.839798 2.51939 3.35919 0 2 3
|
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92 0 2.51939 4.19899 0 2 4
|
||||
97 0 3.35919 3.35919 0 3 3
|
||||
98 0.839798 4.19899 3.35919 0 4 3
|
||||
99 0.839798 3.35919 4.19899 0 3 4
|
||||
100 0 4.19899 4.19899 0 4 4
|
||||
83 1.6796 2.51939 2.51939 1 2 2
|
||||
87 2.51939 3.35919 2.51939 2 3 2
|
||||
88 1.6796 4.19899 2.51939 1 4 2
|
||||
93 2.51939 2.51939 3.35919 2 2 3
|
||||
94 1.6796 2.51939 4.19899 1 2 4
|
||||
101 1.6796 3.35919 3.35919 1 3 3
|
||||
102 2.51939 4.19899 3.35919 2 4 3
|
||||
103 2.51939 3.35919 4.19899 2 3 4
|
||||
104 1.6796 4.19899 4.19899 1 4 4
|
||||
84 3.35919 2.51939 2.51939 3 2 2
|
||||
89 4.19899 3.35919 2.51939 4 3 2
|
||||
90 3.35919 4.19899 2.51939 3 4 2
|
||||
95 4.19899 2.51939 3.35919 4 2 3
|
||||
96 3.35919 2.51939 4.19899 3 2 4
|
||||
105 3.35919 3.35919 3.35919 3 3 3
|
||||
106 4.19899 4.19899 3.35919 4 4 3
|
||||
107 4.19899 3.35919 4.19899 4 3 4
|
||||
108 3.35919 4.19899 4.19899 3 4 4
|
||||
ITEM: TIMESTEP
|
||||
100
|
||||
ITEM: NUMBER OF ATOMS
|
||||
108
|
||||
ITEM: BOX BOUNDS pp pp pp
|
||||
0.0000000000000000e+00 5.0387885741475218e+00
|
||||
0.0000000000000000e+00 5.0387885741475218e+00
|
||||
0.0000000000000000e+00 5.0387885741475218e+00
|
||||
ITEM: ATOMS id x y z v_xtrunc v_ytrunc v_ztrunc
|
||||
27 3.43857 1.71819 1.54054 3 1 1
|
||||
55 1.00239 2.45421 0.0111309 1 2 0
|
||||
24 4.47856 0.849521 1.59138 4 0 1
|
||||
4 5.01236 0.786108 0.77507 5 0 0
|
||||
13 4.90815 1.75715 0.0826318 4 1 0
|
||||
14 0.88902 1.62097 0.874547 0 1 0
|
||||
23 3.50499 0.0189748 1.5186 3 0 1
|
||||
20 0.800033 0.812556 1.72553 0 0 1
|
||||
25 0.149175 1.72252 1.81302 0 1 1
|
||||
18 4.32215 1.8333 0.925663 4 1 0
|
||||
2 0.800305 0.813213 0.0576603 0 0 0
|
||||
11 4.13124 0.178555 0.700886 4 0 0
|
||||
8 1.62464 0.676882 0.777822 1 0 0
|
||||
15 1.54513 1.51174 0.0869798 1 1 0
|
||||
16 2.44634 1.71869 0.918144 2 1 0
|
||||
21 1.77025 0.0864618 1.69637 1 0 1
|
||||
22 2.6077 0.984882 1.7897 2 0 1
|
||||
26 1.75238 1.7433 1.79028 1 1 1
|
||||
56 0.269512 2.41383 0.844638 0 2 0
|
||||
73 0.963279 2.42412 1.76899 0 2 1
|
||||
12 3.22537 0.963341 0.639686 3 0 0
|
||||
29 0.0189933 0.897729 2.4272 0 0 2
|
||||
36 4.12961 1.48438 2.40107 4 1 2
|
||||
31 1.77963 0.875522 2.5056 1 0 2
|
||||
17 3.26063 2.10027 0.0160498 3 2 0
|
||||
32 3.99 0.309367 2.42507 3 0 2
|
||||
10 4.24909 0.985667 5.01613 4 0 5
|
||||
9 3.57018 0.00324557 4.76943 3 0 4
|
||||
34 0.879984 1.74899 2.55389 0 1 2
|
||||
54 4.31748 1.76411 4.20898 4 1 4
|
||||
38 0.833593 0.840282 3.27238 0 0 3
|
||||
53 3.34694 1.70248 3.44784 3 1 3
|
||||
40 0.119704 1.00404 4.09942 0 1 4
|
||||
49 0.0668209 1.77975 3.29313 0 1 3
|
||||
50 0.743432 1.71961 4.3483 0 1 4
|
||||
1 4.97801 0.0605812 4.88474 4 0 4
|
||||
28 0.929754 0.0251285 2.53734 0 0 2
|
||||
94 1.67786 2.47309 4.03082 1 2 4
|
||||
48 3.48471 1.07347 4.35888 3 1 4
|
||||
42 2.34318 0.736887 3.54475 2 0 3
|
||||
46 4.10851 0.877375 3.36388 4 0 3
|
||||
44 1.55893 0.765128 4.31112 1 0 4
|
||||
51 1.73749 1.5259 3.46692 1 1 3
|
||||
52 2.4825 1.46064 4.38907 2 1 4
|
||||
45 3.13128 0.0257347 3.70936 3 0 3
|
||||
33 3.06373 0.748905 2.87477 3 0 2
|
||||
37 4.85349 0.0953155 3.14546 4 0 3
|
||||
95 4.20676 2.29697 3.23228 4 2 3
|
||||
91 0.894798 2.5043 3.34172 0 2 3
|
||||
6 2.46756 0.653742 5.0003 2 0 5
|
||||
35 2.55259 1.72904 2.60295 2 1 2
|
||||
75 4.20455 2.5331 1.87607 4 2 1
|
||||
83 1.7903 2.56204 2.41895 1 2 2
|
||||
90 3.41086 4.28362 2.42553 3 4 2
|
||||
7 2.55699 4.96491 0.926671 2 4 0
|
||||
63 0.867201 3.35405 1.17655 0 3 1
|
||||
64 4.78788 4.34273 0.478103 4 4 0
|
||||
81 4.32623 4.1046 1.69102 4 4 1
|
||||
76 0.0138563 3.23504 1.76147 0 3 1
|
||||
77 0.968224 4.42746 1.67526 0 4 1
|
||||
57 2.0637 2.5991 0.0826392 2 2 0
|
||||
80 3.43363 3.36417 1.87451 3 3 1
|
||||
65 1.42014 3.50181 0.191388 1 3 0
|
||||
58 1.57997 2.52559 1.04361 1 2 1
|
||||
67 2.68157 3.57418 0.921633 2 3 0
|
||||
68 1.77965 4.13041 0.925765 1 4 0
|
||||
74 2.61023 2.6802 1.55816 2 2 1
|
||||
78 1.7741 3.32184 1.66819 1 3 1
|
||||
79 2.4878 4.29352 1.69069 2 4 1
|
||||
59 4.21774 2.61172 0.0367453 4 2 0
|
||||
72 3.52155 4.21032 0.423884 3 4 0
|
||||
19 0.00881412 4.90616 1.74242 0 4 1
|
||||
71 4.2444 3.59428 0.837193 4 3 0
|
||||
60 3.38151 2.6788 0.906258 3 2 0
|
||||
88 1.72356 4.2344 2.49376 1 4 2
|
||||
87 2.56992 3.44579 2.4534 2 3 2
|
||||
61 0.275459 3.26838 0.21932 0 3 0
|
||||
3 0.6485 5.00484 0.836947 0 5 0
|
||||
66 2.39935 4.14279 0.0726977 2 4 0
|
||||
82 0.211736 2.57456 2.48446 0 2 2
|
||||
30 2.55819 4.95626 2.45373 2 4 2
|
||||
108 3.16394 3.96553 4.31023 3 3 4
|
||||
62 0.675354 4.14887 4.94054 0 4 4
|
||||
47 4.30691 4.69041 4.14081 4 4 4
|
||||
107 4.1529 3.22538 3.79605 4 3 3
|
||||
92 0.135168 2.69084 4.12098 0 2 4
|
||||
97 0.0727406 3.44797 3.30247 0 3 3
|
||||
98 1.0752 4.05296 3.38036 1 4 3
|
||||
99 1.0085 3.35058 4.3598 1 3 4
|
||||
100 0.054939 4.00087 4.11831 0 4 4
|
||||
106 4.09781 4.10691 3.24439 4 4 3
|
||||
70 4.24908 3.67507 4.83053 4 3 4
|
||||
43 2.34858 4.82316 4.28272 2 4 4
|
||||
105 3.14646 3.43756 3.28105 3 3 3
|
||||
96 3.1135 2.59262 4.08996 3 2 4
|
||||
101 1.72259 3.24691 3.19685 1 3 3
|
||||
102 2.54324 4.21582 3.29642 2 4 3
|
||||
103 2.33008 3.38603 4.27885 2 3 4
|
||||
104 1.65617 4.10852 4.3491 1 4 4
|
||||
84 3.36606 2.52455 2.67203 3 2 2
|
||||
89 4.22927 3.23505 2.64208 4 3 2
|
||||
41 1.78347 4.95586 3.31184 1 4 3
|
||||
93 2.47391 2.57508 3.27574 2 2 3
|
||||
39 0.578712 4.99093 3.85234 0 4 3
|
||||
86 0.144542 4.27264 2.61793 0 4 2
|
||||
5 1.50261 4.9277 4.9755 1 4 4
|
||||
69 3.10555 3.22911 5.00703 3 3 5
|
||||
85 0.965745 3.43479 2.52674 0 3 2
|
||||
@ -1,9 +1,9 @@
|
||||
# 3d Lennard-Jones melt with equal- and atom-style variables which
|
||||
# use a Python function wrapper in their formulas
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
variable x index 3
|
||||
variable y index 3
|
||||
variable z index 3
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
@ -24,21 +24,37 @@ neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# define Python truncate() function
|
||||
|
||||
variable foo python truncate
|
||||
python truncate return v_foo input 1 iv_arg format fi here """
|
||||
def truncate(x):
|
||||
return int(x)
|
||||
"""
|
||||
|
||||
# use in equal-style variable
|
||||
|
||||
variable scalar equal py_foo(4.5)
|
||||
print "TRUNCATE ${scalar}"
|
||||
|
||||
# use in atom-style variable
|
||||
# examine dump file to see truncated xyz coords of each atom
|
||||
|
||||
variable xtrunc atom py_foo(x)
|
||||
variable ytrunc atom py_foo(y)
|
||||
variable ztrunc atom py_foo(z)
|
||||
|
||||
# examine dump file to see truncated xyz coords of each atom
|
||||
|
||||
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
|
||||
|
||||
# use in vector-style variable
|
||||
|
||||
compute ke all temp
|
||||
variable ke vector c_ke
|
||||
variable ketrunc vector py_foo(v_ke)
|
||||
thermo_style custom step temp epair v_ketrunc[*6]
|
||||
|
||||
run 100
|
||||
|
||||
print "KE TENSOR ${ketrunc}"
|
||||
|
||||
|
||||
|
||||
@ -1,10 +1,10 @@
|
||||
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified)
|
||||
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-270-g2351418c94-modified)
|
||||
# 3d Lennard-Jones melt with equal- and atom-style variables which
|
||||
# use a Python function wrapper in their formulas
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
variable x index 3
|
||||
variable y index 3
|
||||
variable z index 3
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
@ -12,15 +12,15 @@ atom_style atomic
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
region box block 0 3 0 $y 0 $z
|
||||
region box block 0 3 0 3 0 $z
|
||||
region box block 0 3 0 3 0 3
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
Created 108 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
@ -34,24 +34,36 @@ neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# define Python truncate() function
|
||||
|
||||
variable foo python truncate
|
||||
python truncate return v_foo input 1 iv_arg format fi here """
|
||||
def truncate(x):
|
||||
return int(x)
|
||||
"""
|
||||
|
||||
# use in equal-style variable
|
||||
|
||||
variable scalar equal py_foo(4.5)
|
||||
print "TRUNCATE ${scalar}"
|
||||
TRUNCATE 4
|
||||
|
||||
# use in atom-style variable
|
||||
# examine dump file to see truncated xyz coords of each atom
|
||||
|
||||
variable xtrunc atom py_foo(x)
|
||||
variable ytrunc atom py_foo(y)
|
||||
variable ztrunc atom py_foo(z)
|
||||
|
||||
# examine dump file to see truncated xyz coords of each atom
|
||||
|
||||
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
|
||||
|
||||
# use in vector-style variable
|
||||
|
||||
compute ke all temp
|
||||
variable ke vector c_ke
|
||||
variable ketrunc vector py_foo(v_ke)
|
||||
thermo_style custom step temp epair v_ketrunc[*6]
|
||||
|
||||
run 100
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
@ -59,41 +71,46 @@ Neighbor list info ...
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
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) = 2.644 | 2.644 | 2.644 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
100 0.75627408 -5.7580082 0 -4.6258659 0.21870071
|
||||
Loop time of 0.014627 on 1 procs for 100 steps with 500 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.598 | 2.598 | 2.598 Mbytes
|
||||
Step Temp E_pair v_ketrunc[1] v_ketrunc[2] v_ketrunc[3] v_ketrunc[4] v_ketrunc[5] v_ketrunc[6]
|
||||
0 1.44 -6.7733681 155 152 154 -10 -4 -6
|
||||
100 0.82217015 -5.8614684 113 65 84 7 -1 -12
|
||||
Loop time of 0.00278186 on 1 procs for 100 steps with 108 atoms
|
||||
|
||||
Performance: 2953445.899 tau/day, 6836.680 timesteps/s, 3.418 Matom-step/s
|
||||
Performance: 15529161.573 tau/day, 35947.133 timesteps/s, 3.882 Matom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.010546 | 0.010546 | 0.010546 | 0.0 | 72.10
|
||||
Neigh | 0.0027775 | 0.0027775 | 0.0027775 | 0.0 | 18.99
|
||||
Comm | 0.00044818 | 0.00044818 | 0.00044818 | 0.0 | 3.06
|
||||
Output | 0.00060601 | 0.00060601 | 0.00060601 | 0.0 | 4.14
|
||||
Modify | 0.00018516 | 0.00018516 | 0.00018516 | 0.0 | 1.27
|
||||
Other | | 6.39e-05 | | | 0.44
|
||||
Pair | 0.0018161 | 0.0018161 | 0.0018161 | 0.0 | 65.29
|
||||
Neigh | 0.00057543 | 0.00057543 | 0.00057543 | 0.0 | 20.68
|
||||
Comm | 0.00019634 | 0.00019634 | 0.00019634 | 0.0 | 7.06
|
||||
Output | 0.00012056 | 0.00012056 | 0.00012056 | 0.0 | 4.33
|
||||
Modify | 4.8221e-05 | 4.8221e-05 | 4.8221e-05 | 0.0 | 1.73
|
||||
Other | | 2.516e-05 | | | 0.90
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Nlocal: 108 ave 108 max 108 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1941 ave 1941 max 1941 min
|
||||
Nghost: 980 ave 980 max 980 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18766 ave 18766 max 18766 min
|
||||
Neighs: 4071 ave 4071 max 4071 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18766
|
||||
Ave neighs/atom = 37.532
|
||||
Total # of neighbors = 4071
|
||||
Ave neighs/atom = 37.694444
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
|
||||
print "KE TENSOR ${ketrunc}"
|
||||
KE TENSOR [113,65,84,7,-1,-12]
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
||||
@ -1,10 +1,10 @@
|
||||
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified)
|
||||
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-270-g2351418c94-modified)
|
||||
# 3d Lennard-Jones melt with equal- and atom-style variables which
|
||||
# use a Python function wrapper in their formulas
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
variable x index 3
|
||||
variable y index 3
|
||||
variable z index 3
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
@ -12,15 +12,15 @@ atom_style atomic
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
region box block 0 3 0 $y 0 $z
|
||||
region box block 0 3 0 3 0 $z
|
||||
region box block 0 3 0 3 0 3
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
Created 108 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
@ -34,24 +34,36 @@ neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# define Python truncate() function
|
||||
|
||||
variable foo python truncate
|
||||
python truncate return v_foo input 1 iv_arg format fi here """
|
||||
def truncate(x):
|
||||
return int(x)
|
||||
"""
|
||||
|
||||
# use in equal-style variable
|
||||
|
||||
variable scalar equal py_foo(4.5)
|
||||
print "TRUNCATE ${scalar}"
|
||||
TRUNCATE 4
|
||||
|
||||
# use in atom-style variable
|
||||
# examine dump file to see truncated xyz coords of each atom
|
||||
|
||||
variable xtrunc atom py_foo(x)
|
||||
variable ytrunc atom py_foo(y)
|
||||
variable ztrunc atom py_foo(z)
|
||||
|
||||
# examine dump file to see truncated xyz coords of each atom
|
||||
|
||||
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
|
||||
|
||||
# use in vector-style variable
|
||||
|
||||
compute ke all temp
|
||||
variable ke vector c_ke
|
||||
variable ketrunc vector py_foo(v_ke)
|
||||
thermo_style custom step temp epair v_ketrunc[*6]
|
||||
|
||||
run 100
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
@ -59,41 +71,46 @@ Neighbor list info ...
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
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) = 2.609 | 2.609 | 2.609 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
100 0.75627408 -5.7580082 0 -4.6258659 0.21870071
|
||||
Loop time of 0.0062374 on 4 procs for 100 steps with 500 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.59 | 2.59 | 2.59 Mbytes
|
||||
Step Temp E_pair v_ketrunc[1] v_ketrunc[2] v_ketrunc[3] v_ketrunc[4] v_ketrunc[5] v_ketrunc[6]
|
||||
0 1.44 -6.7733681 155 152 154 -10 -4 -6
|
||||
100 0.82217015 -5.8614684 113 65 84 7 -1 -12
|
||||
Loop time of 0.00268845 on 4 procs for 100 steps with 108 atoms
|
||||
|
||||
Performance: 6925957.189 tau/day, 16032.308 timesteps/s, 8.016 Matom-step/s
|
||||
74.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 16068745.964 tau/day, 37196.171 timesteps/s, 4.017 Matom-step/s
|
||||
66.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0027648 | 0.0028431 | 0.0029465 | 0.1 | 45.58
|
||||
Neigh | 0.00084567 | 0.00086563 | 0.00088168 | 0.0 | 13.88
|
||||
Comm | 0.0020822 | 0.0021609 | 0.0022418 | 0.1 | 34.64
|
||||
Output | 0.00021567 | 0.00022125 | 0.00022624 | 0.0 | 3.55
|
||||
Modify | 6.2567e-05 | 6.4105e-05 | 6.63e-05 | 0.0 | 1.03
|
||||
Other | | 8.241e-05 | | | 1.32
|
||||
Pair | 0.00043389 | 0.00051695 | 0.00061255 | 0.0 | 19.23
|
||||
Neigh | 0.00017121 | 0.00018976 | 0.00019891 | 0.0 | 7.06
|
||||
Comm | 0.0017423 | 0.0018487 | 0.0019509 | 0.2 | 68.76
|
||||
Output | 6.7449e-05 | 6.9998e-05 | 7.5195e-05 | 0.0 | 2.60
|
||||
Modify | 2.1329e-05 | 2.2855e-05 | 2.4821e-05 | 0.0 | 0.85
|
||||
Other | | 4.018e-05 | | | 1.49
|
||||
|
||||
Nlocal: 125 ave 126 max 123 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 1085.75 ave 1090 max 1082 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 4691.5 ave 4969 max 4368 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nlocal: 27 ave 30 max 25 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 614 ave 616 max 612 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 1017.75 ave 1149 max 894 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 18766
|
||||
Ave neighs/atom = 37.532
|
||||
Total # of neighbors = 4071
|
||||
Ave neighs/atom = 37.694444
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
|
||||
print "KE TENSOR ${ketrunc}"
|
||||
KE TENSOR [113,65,84,7,-1,-12]
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
||||
Reference in New Issue
Block a user