updated fix_langevin and made example
This commit is contained in:
casievers
886
examples/gjf/argon.lmp
Normal file
886
examples/gjf/argon.lmp
Normal file
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LAMMPS description
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864 atoms
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0 bonds
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0 angles
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0 dihedrals
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0 impropers
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1 atom types
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0 bond types
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0 angle types
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0 dihedral types
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0 improper types
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0.0000000 32.146000 xlo xhi
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0.0000000 32.146000 ylo yhi
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0.0000000 32.146000 zlo zhi
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Atoms
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1 1 1 0.0000000 0.0000000 2.6790000 2.6790000
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2 2 1 0.0000000 0.0000000 2.6790000 8.0360000
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3 3 1 0.0000000 0.0000000 2.6790000 13.3940000
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4 4 1 0.0000000 0.0000000 2.6790000 18.7520000
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5 5 1 0.0000000 0.0000000 2.6790000 24.1090000
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6 6 1 0.0000000 0.0000000 2.6790000 29.4670000
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7 7 1 0.0000000 0.0000000 8.0360000 2.6790000
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8 8 1 0.0000000 0.0000000 8.0360000 8.0360000
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9 9 1 0.0000000 0.0000000 8.0360000 13.3940000
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10 10 1 0.0000000 0.0000000 8.0360000 18.7520000
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11 11 1 0.0000000 0.0000000 8.0360000 24.1090000
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12 12 1 0.0000000 0.0000000 8.0360000 29.4670000
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13 13 1 0.0000000 0.0000000 13.3940000 2.6790000
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14 14 1 0.0000000 0.0000000 13.3940000 8.0360000
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15 15 1 0.0000000 0.0000000 13.3940000 13.3940000
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16 16 1 0.0000000 0.0000000 13.3940000 18.7520000
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17 17 1 0.0000000 0.0000000 13.3940000 24.1090000
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18 18 1 0.0000000 0.0000000 13.3940000 29.4670000
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19 19 1 0.0000000 0.0000000 18.7520000 2.6790000
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20 20 1 0.0000000 0.0000000 18.7520000 8.0360000
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21 21 1 0.0000000 0.0000000 18.7520000 13.3940000
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22 22 1 0.0000000 0.0000000 18.7520000 18.7520000
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23 23 1 0.0000000 0.0000000 18.7520000 24.1090000
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24 24 1 0.0000000 0.0000000 18.7520000 29.4670000
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25 25 1 0.0000000 0.0000000 24.1090000 2.6790000
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26 26 1 0.0000000 0.0000000 24.1090000 8.0360000
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27 27 1 0.0000000 0.0000000 24.1090000 13.3940000
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28 28 1 0.0000000 0.0000000 24.1090000 18.7520000
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29 29 1 0.0000000 0.0000000 24.1090000 24.1090000
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30 30 1 0.0000000 0.0000000 24.1090000 29.4670000
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31 31 1 0.0000000 0.0000000 29.4670000 2.6790000
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32 32 1 0.0000000 0.0000000 29.4670000 8.0360000
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33 33 1 0.0000000 0.0000000 29.4670000 13.3940000
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34 34 1 0.0000000 0.0000000 29.4670000 18.7520000
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35 35 1 0.0000000 0.0000000 29.4670000 24.1090000
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36 36 1 0.0000000 0.0000000 29.4670000 29.4670000
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||||||
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37 37 1 0.0000000 5.3580000 2.6790000 2.6790000
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38 38 1 0.0000000 5.3580000 2.6790000 8.0360000
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||||||
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39 39 1 0.0000000 5.3580000 2.6790000 13.3940000
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||||||
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40 40 1 0.0000000 5.3580000 2.6790000 18.7520000
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||||||
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41 41 1 0.0000000 5.3580000 2.6790000 24.1090000
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42 42 1 0.0000000 5.3580000 2.6790000 29.4670000
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||||||
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43 43 1 0.0000000 5.3580000 8.0360000 2.6790000
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44 44 1 0.0000000 5.3580000 8.0360000 8.0360000
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45 45 1 0.0000000 5.3580000 8.0360000 13.3940000
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46 46 1 0.0000000 5.3580000 8.0360000 18.7520000
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||||||
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47 47 1 0.0000000 5.3580000 8.0360000 24.1090000
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48 48 1 0.0000000 5.3580000 8.0360000 29.4670000
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49 49 1 0.0000000 5.3580000 13.3940000 2.6790000
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50 50 1 0.0000000 5.3580000 13.3940000 8.0360000
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51 51 1 0.0000000 5.3580000 13.3940000 13.3940000
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52 52 1 0.0000000 5.3580000 13.3940000 18.7520000
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53 53 1 0.0000000 5.3580000 13.3940000 24.1090000
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54 54 1 0.0000000 5.3580000 13.3940000 29.4670000
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55 55 1 0.0000000 5.3580000 18.7520000 2.6790000
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56 56 1 0.0000000 5.3580000 18.7520000 8.0360000
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57 57 1 0.0000000 5.3580000 18.7520000 13.3940000
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58 58 1 0.0000000 5.3580000 18.7520000 18.7520000
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59 59 1 0.0000000 5.3580000 18.7520000 24.1090000
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60 60 1 0.0000000 5.3580000 18.7520000 29.4670000
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61 61 1 0.0000000 5.3580000 24.1090000 2.6790000
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62 62 1 0.0000000 5.3580000 24.1090000 8.0360000
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63 63 1 0.0000000 5.3580000 24.1090000 13.3940000
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64 64 1 0.0000000 5.3580000 24.1090000 18.7520000
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65 65 1 0.0000000 5.3580000 24.1090000 24.1090000
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66 66 1 0.0000000 5.3580000 24.1090000 29.4670000
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67 67 1 0.0000000 5.3580000 29.4670000 2.6790000
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68 68 1 0.0000000 5.3580000 29.4670000 8.0360000
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69 69 1 0.0000000 5.3580000 29.4670000 13.3940000
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70 70 1 0.0000000 5.3580000 29.4670000 18.7520000
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71 71 1 0.0000000 5.3580000 29.4670000 24.1090000
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72 72 1 0.0000000 5.3580000 29.4670000 29.4670000
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73 73 1 0.0000000 10.7150000 2.6790000 2.6790000
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74 74 1 0.0000000 10.7150000 2.6790000 8.0360000
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75 75 1 0.0000000 10.7150000 2.6790000 13.3940000
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76 76 1 0.0000000 10.7150000 2.6790000 18.7520000
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77 77 1 0.0000000 10.7150000 2.6790000 24.1090000
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78 78 1 0.0000000 10.7150000 2.6790000 29.4670000
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79 79 1 0.0000000 10.7150000 8.0360000 2.6790000
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80 80 1 0.0000000 10.7150000 8.0360000 8.0360000
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81 81 1 0.0000000 10.7150000 8.0360000 13.3940000
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82 82 1 0.0000000 10.7150000 8.0360000 18.7520000
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83 83 1 0.0000000 10.7150000 8.0360000 24.1090000
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84 84 1 0.0000000 10.7150000 8.0360000 29.4670000
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85 85 1 0.0000000 10.7150000 13.3940000 2.6790000
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86 86 1 0.0000000 10.7150000 13.3940000 8.0360000
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87 87 1 0.0000000 10.7150000 13.3940000 13.3940000
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88 88 1 0.0000000 10.7150000 13.3940000 18.7520000
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89 89 1 0.0000000 10.7150000 13.3940000 24.1090000
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90 90 1 0.0000000 10.7150000 13.3940000 29.4670000
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91 91 1 0.0000000 10.7150000 18.7520000 2.6790000
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92 92 1 0.0000000 10.7150000 18.7520000 8.0360000
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93 93 1 0.0000000 10.7150000 18.7520000 13.3940000
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94 94 1 0.0000000 10.7150000 18.7520000 18.7520000
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95 95 1 0.0000000 10.7150000 18.7520000 24.1090000
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96 96 1 0.0000000 10.7150000 18.7520000 29.4670000
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97 97 1 0.0000000 10.7150000 24.1090000 2.6790000
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98 98 1 0.0000000 10.7150000 24.1090000 8.0360000
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99 99 1 0.0000000 10.7150000 24.1090000 13.3940000
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100 100 1 0.0000000 10.7150000 24.1090000 18.7520000
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101 101 1 0.0000000 10.7150000 24.1090000 24.1090000
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102 102 1 0.0000000 10.7150000 24.1090000 29.4670000
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103 103 1 0.0000000 10.7150000 29.4670000 2.6790000
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104 104 1 0.0000000 10.7150000 29.4670000 8.0360000
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105 105 1 0.0000000 10.7150000 29.4670000 13.3940000
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106 106 1 0.0000000 10.7150000 29.4670000 18.7520000
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107 107 1 0.0000000 10.7150000 29.4670000 24.1090000
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108 108 1 0.0000000 10.7150000 29.4670000 29.4670000
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109 109 1 0.0000000 16.0730000 2.6790000 2.6790000
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110 110 1 0.0000000 16.0730000 2.6790000 8.0360000
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111 111 1 0.0000000 16.0730000 2.6790000 13.3940000
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112 112 1 0.0000000 16.0730000 2.6790000 18.7520000
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113 113 1 0.0000000 16.0730000 2.6790000 24.1090000
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114 114 1 0.0000000 16.0730000 2.6790000 29.4670000
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115 115 1 0.0000000 16.0730000 8.0360000 2.6790000
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116 116 1 0.0000000 16.0730000 8.0360000 8.0360000
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117 117 1 0.0000000 16.0730000 8.0360000 13.3940000
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118 118 1 0.0000000 16.0730000 8.0360000 18.7520000
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119 119 1 0.0000000 16.0730000 8.0360000 24.1090000
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120 120 1 0.0000000 16.0730000 8.0360000 29.4670000
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121 121 1 0.0000000 16.0730000 13.3940000 2.6790000
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122 122 1 0.0000000 16.0730000 13.3940000 8.0360000
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123 123 1 0.0000000 16.0730000 13.3940000 13.3940000
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124 124 1 0.0000000 16.0730000 13.3940000 18.7520000
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125 125 1 0.0000000 16.0730000 13.3940000 24.1090000
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126 126 1 0.0000000 16.0730000 13.3940000 29.4670000
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127 127 1 0.0000000 16.0730000 18.7520000 2.6790000
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128 128 1 0.0000000 16.0730000 18.7520000 8.0360000
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129 129 1 0.0000000 16.0730000 18.7520000 13.3940000
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130 130 1 0.0000000 16.0730000 18.7520000 18.7520000
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131 131 1 0.0000000 16.0730000 18.7520000 24.1090000
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132 132 1 0.0000000 16.0730000 18.7520000 29.4670000
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133 133 1 0.0000000 16.0730000 24.1090000 2.6790000
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134 134 1 0.0000000 16.0730000 24.1090000 8.0360000
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135 135 1 0.0000000 16.0730000 24.1090000 13.3940000
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136 136 1 0.0000000 16.0730000 24.1090000 18.7520000
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137 137 1 0.0000000 16.0730000 24.1090000 24.1090000
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138 138 1 0.0000000 16.0730000 24.1090000 29.4670000
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139 139 1 0.0000000 16.0730000 29.4670000 2.6790000
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140 140 1 0.0000000 16.0730000 29.4670000 8.0360000
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141 141 1 0.0000000 16.0730000 29.4670000 13.3940000
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142 142 1 0.0000000 16.0730000 29.4670000 18.7520000
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143 143 1 0.0000000 16.0730000 29.4670000 24.1090000
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144 144 1 0.0000000 16.0730000 29.4670000 29.4670000
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145 145 1 0.0000000 21.4310000 2.6790000 2.6790000
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146 146 1 0.0000000 21.4310000 2.6790000 8.0360000
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147 147 1 0.0000000 21.4310000 2.6790000 13.3940000
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148 148 1 0.0000000 21.4310000 2.6790000 18.7520000
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149 149 1 0.0000000 21.4310000 2.6790000 24.1090000
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150 150 1 0.0000000 21.4310000 2.6790000 29.4670000
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151 151 1 0.0000000 21.4310000 8.0360000 2.6790000
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152 152 1 0.0000000 21.4310000 8.0360000 8.0360000
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153 153 1 0.0000000 21.4310000 8.0360000 13.3940000
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154 154 1 0.0000000 21.4310000 8.0360000 18.7520000
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155 155 1 0.0000000 21.4310000 8.0360000 24.1090000
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156 156 1 0.0000000 21.4310000 8.0360000 29.4670000
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157 157 1 0.0000000 21.4310000 13.3940000 2.6790000
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158 158 1 0.0000000 21.4310000 13.3940000 8.0360000
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159 159 1 0.0000000 21.4310000 13.3940000 13.3940000
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160 160 1 0.0000000 21.4310000 13.3940000 18.7520000
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161 161 1 0.0000000 21.4310000 13.3940000 24.1090000
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162 162 1 0.0000000 21.4310000 13.3940000 29.4670000
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163 163 1 0.0000000 21.4310000 18.7520000 2.6790000
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164 164 1 0.0000000 21.4310000 18.7520000 8.0360000
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165 165 1 0.0000000 21.4310000 18.7520000 13.3940000
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166 166 1 0.0000000 21.4310000 18.7520000 18.7520000
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167 167 1 0.0000000 21.4310000 18.7520000 24.1090000
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168 168 1 0.0000000 21.4310000 18.7520000 29.4670000
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169 169 1 0.0000000 21.4310000 24.1090000 2.6790000
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170 170 1 0.0000000 21.4310000 24.1090000 8.0360000
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171 171 1 0.0000000 21.4310000 24.1090000 13.3940000
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172 172 1 0.0000000 21.4310000 24.1090000 18.7520000
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173 173 1 0.0000000 21.4310000 24.1090000 24.1090000
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174 174 1 0.0000000 21.4310000 24.1090000 29.4670000
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175 175 1 0.0000000 21.4310000 29.4670000 2.6790000
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176 176 1 0.0000000 21.4310000 29.4670000 8.0360000
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177 177 1 0.0000000 21.4310000 29.4670000 13.3940000
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178 178 1 0.0000000 21.4310000 29.4670000 18.7520000
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179 179 1 0.0000000 21.4310000 29.4670000 24.1090000
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180 180 1 0.0000000 21.4310000 29.4670000 29.4670000
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181 181 1 0.0000000 26.7880000 2.6790000 2.6790000
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182 182 1 0.0000000 26.7880000 2.6790000 8.0360000
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183 183 1 0.0000000 26.7880000 2.6790000 13.3940000
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184 184 1 0.0000000 26.7880000 2.6790000 18.7520000
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185 185 1 0.0000000 26.7880000 2.6790000 24.1090000
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186 186 1 0.0000000 26.7880000 2.6790000 29.4670000
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187 187 1 0.0000000 26.7880000 8.0360000 2.6790000
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188 188 1 0.0000000 26.7880000 8.0360000 8.0360000
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189 189 1 0.0000000 26.7880000 8.0360000 13.3940000
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190 190 1 0.0000000 26.7880000 8.0360000 18.7520000
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191 191 1 0.0000000 26.7880000 8.0360000 24.1090000
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192 192 1 0.0000000 26.7880000 8.0360000 29.4670000
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193 193 1 0.0000000 26.7880000 13.3940000 2.6790000
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194 194 1 0.0000000 26.7880000 13.3940000 8.0360000
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195 195 1 0.0000000 26.7880000 13.3940000 13.3940000
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196 196 1 0.0000000 26.7880000 13.3940000 18.7520000
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197 197 1 0.0000000 26.7880000 13.3940000 24.1090000
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198 198 1 0.0000000 26.7880000 13.3940000 29.4670000
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199 199 1 0.0000000 26.7880000 18.7520000 2.6790000
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200 200 1 0.0000000 26.7880000 18.7520000 8.0360000
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201 201 1 0.0000000 26.7880000 18.7520000 13.3940000
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202 202 1 0.0000000 26.7880000 18.7520000 18.7520000
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203 203 1 0.0000000 26.7880000 18.7520000 24.1090000
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204 204 1 0.0000000 26.7880000 18.7520000 29.4670000
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205 205 1 0.0000000 26.7880000 24.1090000 2.6790000
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206 206 1 0.0000000 26.7880000 24.1090000 8.0360000
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207 207 1 0.0000000 26.7880000 24.1090000 13.3940000
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208 208 1 0.0000000 26.7880000 24.1090000 18.7520000
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209 209 1 0.0000000 26.7880000 24.1090000 24.1090000
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210 210 1 0.0000000 26.7880000 24.1090000 29.4670000
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211 211 1 0.0000000 26.7880000 29.4670000 2.6790000
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212 212 1 0.0000000 26.7880000 29.4670000 8.0360000
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213 213 1 0.0000000 26.7880000 29.4670000 13.3940000
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214 214 1 0.0000000 26.7880000 29.4670000 18.7520000
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215 215 1 0.0000000 26.7880000 29.4670000 24.1090000
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216 216 1 0.0000000 26.7880000 29.4670000 29.4670000
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217 217 1 0.0000000 2.6790000 5.3580000 2.6790000
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218 218 1 0.0000000 2.6790000 5.3580000 8.0360000
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219 219 1 0.0000000 2.6790000 5.3580000 13.3940000
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220 220 1 0.0000000 2.6790000 5.3580000 18.7520000
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221 221 1 0.0000000 2.6790000 5.3580000 24.1090000
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222 222 1 0.0000000 2.6790000 5.3580000 29.4670000
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223 223 1 0.0000000 2.6790000 10.7150000 2.6790000
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224 224 1 0.0000000 2.6790000 10.7150000 8.0360000
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225 225 1 0.0000000 2.6790000 10.7150000 13.3940000
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226 226 1 0.0000000 2.6790000 10.7150000 18.7520000
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227 227 1 0.0000000 2.6790000 10.7150000 24.1090000
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228 228 1 0.0000000 2.6790000 10.7150000 29.4670000
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229 229 1 0.0000000 2.6790000 16.0730000 2.6790000
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230 230 1 0.0000000 2.6790000 16.0730000 8.0360000
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231 231 1 0.0000000 2.6790000 16.0730000 13.3940000
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232 232 1 0.0000000 2.6790000 16.0730000 18.7520000
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233 233 1 0.0000000 2.6790000 16.0730000 24.1090000
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234 234 1 0.0000000 2.6790000 16.0730000 29.4670000
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235 235 1 0.0000000 2.6790000 21.4310000 2.6790000
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236 236 1 0.0000000 2.6790000 21.4310000 8.0360000
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237 237 1 0.0000000 2.6790000 21.4310000 13.3940000
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238 238 1 0.0000000 2.6790000 21.4310000 18.7520000
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239 239 1 0.0000000 2.6790000 21.4310000 24.1090000
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240 240 1 0.0000000 2.6790000 21.4310000 29.4670000
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241 241 1 0.0000000 2.6790000 26.7880000 2.6790000
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242 242 1 0.0000000 2.6790000 26.7880000 8.0360000
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243 243 1 0.0000000 2.6790000 26.7880000 13.3940000
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244 244 1 0.0000000 2.6790000 26.7880000 18.7520000
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245 245 1 0.0000000 2.6790000 26.7880000 24.1090000
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246 246 1 0.0000000 2.6790000 26.7880000 29.4670000
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247 247 1 0.0000000 2.6790000 32.1460000 2.6790000
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248 248 1 0.0000000 2.6790000 32.1460000 8.0360000
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249 249 1 0.0000000 2.6790000 32.1460000 13.3940000
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250 250 1 0.0000000 2.6790000 32.1460000 18.7520000
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||||||
|
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||||||
|
770 770 1 0.0000000 16.0730000 16.0730000 10.7150000
|
||||||
|
771 771 1 0.0000000 16.0730000 16.0730000 16.0730000
|
||||||
|
772 772 1 0.0000000 16.0730000 16.0730000 21.4310000
|
||||||
|
773 773 1 0.0000000 16.0730000 16.0730000 26.7880000
|
||||||
|
774 774 1 0.0000000 16.0730000 16.0730000 32.1460000
|
||||||
|
775 775 1 0.0000000 16.0730000 21.4310000 5.3580000
|
||||||
|
776 776 1 0.0000000 16.0730000 21.4310000 10.7150000
|
||||||
|
777 777 1 0.0000000 16.0730000 21.4310000 16.0730000
|
||||||
|
778 778 1 0.0000000 16.0730000 21.4310000 21.4310000
|
||||||
|
779 779 1 0.0000000 16.0730000 21.4310000 26.7880000
|
||||||
|
780 780 1 0.0000000 16.0730000 21.4310000 32.1460000
|
||||||
|
781 781 1 0.0000000 16.0730000 26.7880000 5.3580000
|
||||||
|
782 782 1 0.0000000 16.0730000 26.7880000 10.7150000
|
||||||
|
783 783 1 0.0000000 16.0730000 26.7880000 16.0730000
|
||||||
|
784 784 1 0.0000000 16.0730000 26.7880000 21.4310000
|
||||||
|
785 785 1 0.0000000 16.0730000 26.7880000 26.7880000
|
||||||
|
786 786 1 0.0000000 16.0730000 26.7880000 32.1460000
|
||||||
|
787 787 1 0.0000000 16.0730000 32.1460000 5.3580000
|
||||||
|
788 788 1 0.0000000 16.0730000 32.1460000 10.7150000
|
||||||
|
789 789 1 0.0000000 16.0730000 32.1460000 16.0730000
|
||||||
|
790 790 1 0.0000000 16.0730000 32.1460000 21.4310000
|
||||||
|
791 791 1 0.0000000 16.0730000 32.1460000 26.7880000
|
||||||
|
792 792 1 0.0000000 16.0730000 32.1460000 32.1460000
|
||||||
|
793 793 1 0.0000000 21.4310000 5.3580000 5.3580000
|
||||||
|
794 794 1 0.0000000 21.4310000 5.3580000 10.7150000
|
||||||
|
795 795 1 0.0000000 21.4310000 5.3580000 16.0730000
|
||||||
|
796 796 1 0.0000000 21.4310000 5.3580000 21.4310000
|
||||||
|
797 797 1 0.0000000 21.4310000 5.3580000 26.7880000
|
||||||
|
798 798 1 0.0000000 21.4310000 5.3580000 32.1460000
|
||||||
|
799 799 1 0.0000000 21.4310000 10.7150000 5.3580000
|
||||||
|
800 800 1 0.0000000 21.4310000 10.7150000 10.7150000
|
||||||
|
801 801 1 0.0000000 21.4310000 10.7150000 16.0730000
|
||||||
|
802 802 1 0.0000000 21.4310000 10.7150000 21.4310000
|
||||||
|
803 803 1 0.0000000 21.4310000 10.7150000 26.7880000
|
||||||
|
804 804 1 0.0000000 21.4310000 10.7150000 32.1460000
|
||||||
|
805 805 1 0.0000000 21.4310000 16.0730000 5.3580000
|
||||||
|
806 806 1 0.0000000 21.4310000 16.0730000 10.7150000
|
||||||
|
807 807 1 0.0000000 21.4310000 16.0730000 16.0730000
|
||||||
|
808 808 1 0.0000000 21.4310000 16.0730000 21.4310000
|
||||||
|
809 809 1 0.0000000 21.4310000 16.0730000 26.7880000
|
||||||
|
810 810 1 0.0000000 21.4310000 16.0730000 32.1460000
|
||||||
|
811 811 1 0.0000000 21.4310000 21.4310000 5.3580000
|
||||||
|
812 812 1 0.0000000 21.4310000 21.4310000 10.7150000
|
||||||
|
813 813 1 0.0000000 21.4310000 21.4310000 16.0730000
|
||||||
|
814 814 1 0.0000000 21.4310000 21.4310000 21.4310000
|
||||||
|
815 815 1 0.0000000 21.4310000 21.4310000 26.7880000
|
||||||
|
816 816 1 0.0000000 21.4310000 21.4310000 32.1460000
|
||||||
|
817 817 1 0.0000000 21.4310000 26.7880000 5.3580000
|
||||||
|
818 818 1 0.0000000 21.4310000 26.7880000 10.7150000
|
||||||
|
819 819 1 0.0000000 21.4310000 26.7880000 16.0730000
|
||||||
|
820 820 1 0.0000000 21.4310000 26.7880000 21.4310000
|
||||||
|
821 821 1 0.0000000 21.4310000 26.7880000 26.7880000
|
||||||
|
822 822 1 0.0000000 21.4310000 26.7880000 32.1460000
|
||||||
|
823 823 1 0.0000000 21.4310000 32.1460000 5.3580000
|
||||||
|
824 824 1 0.0000000 21.4310000 32.1460000 10.7150000
|
||||||
|
825 825 1 0.0000000 21.4310000 32.1460000 16.0730000
|
||||||
|
826 826 1 0.0000000 21.4310000 32.1460000 21.4310000
|
||||||
|
827 827 1 0.0000000 21.4310000 32.1460000 26.7880000
|
||||||
|
828 828 1 0.0000000 21.4310000 32.1460000 32.1460000
|
||||||
|
829 829 1 0.0000000 26.7880000 5.3580000 5.3580000
|
||||||
|
830 830 1 0.0000000 26.7880000 5.3580000 10.7150000
|
||||||
|
831 831 1 0.0000000 26.7880000 5.3580000 16.0730000
|
||||||
|
832 832 1 0.0000000 26.7880000 5.3580000 21.4310000
|
||||||
|
833 833 1 0.0000000 26.7880000 5.3580000 26.7880000
|
||||||
|
834 834 1 0.0000000 26.7880000 5.3580000 32.1460000
|
||||||
|
835 835 1 0.0000000 26.7880000 10.7150000 5.3580000
|
||||||
|
836 836 1 0.0000000 26.7880000 10.7150000 10.7150000
|
||||||
|
837 837 1 0.0000000 26.7880000 10.7150000 16.0730000
|
||||||
|
838 838 1 0.0000000 26.7880000 10.7150000 21.4310000
|
||||||
|
839 839 1 0.0000000 26.7880000 10.7150000 26.7880000
|
||||||
|
840 840 1 0.0000000 26.7880000 10.7150000 32.1460000
|
||||||
|
841 841 1 0.0000000 26.7880000 16.0730000 5.3580000
|
||||||
|
842 842 1 0.0000000 26.7880000 16.0730000 10.7150000
|
||||||
|
843 843 1 0.0000000 26.7880000 16.0730000 16.0730000
|
||||||
|
844 844 1 0.0000000 26.7880000 16.0730000 21.4310000
|
||||||
|
845 845 1 0.0000000 26.7880000 16.0730000 26.7880000
|
||||||
|
846 846 1 0.0000000 26.7880000 16.0730000 32.1460000
|
||||||
|
847 847 1 0.0000000 26.7880000 21.4310000 5.3580000
|
||||||
|
848 848 1 0.0000000 26.7880000 21.4310000 10.7150000
|
||||||
|
849 849 1 0.0000000 26.7880000 21.4310000 16.0730000
|
||||||
|
850 850 1 0.0000000 26.7880000 21.4310000 21.4310000
|
||||||
|
851 851 1 0.0000000 26.7880000 21.4310000 26.7880000
|
||||||
|
852 852 1 0.0000000 26.7880000 21.4310000 32.1460000
|
||||||
|
853 853 1 0.0000000 26.7880000 26.7880000 5.3580000
|
||||||
|
854 854 1 0.0000000 26.7880000 26.7880000 10.7150000
|
||||||
|
855 855 1 0.0000000 26.7880000 26.7880000 16.0730000
|
||||||
|
856 856 1 0.0000000 26.7880000 26.7880000 21.4310000
|
||||||
|
857 857 1 0.0000000 26.7880000 26.7880000 26.7880000
|
||||||
|
858 858 1 0.0000000 26.7880000 26.7880000 32.1460000
|
||||||
|
859 859 1 0.0000000 26.7880000 32.1460000 5.3580000
|
||||||
|
860 860 1 0.0000000 26.7880000 32.1460000 10.7150000
|
||||||
|
861 861 1 0.0000000 26.7880000 32.1460000 16.0730000
|
||||||
|
862 862 1 0.0000000 26.7880000 32.1460000 21.4310000
|
||||||
|
863 863 1 0.0000000 26.7880000 32.1460000 26.7880000
|
||||||
|
864 864 1 0.0000000 26.7880000 32.1460000 32.1460000
|
||||||
|
|
||||||
20
examples/gjf/ff-argon.lmp
Normal file
20
examples/gjf/ff-argon.lmp
Normal file
@ -0,0 +1,20 @@
|
|||||||
|
#############################
|
||||||
|
#Atoms types - mass - charge#
|
||||||
|
#############################
|
||||||
|
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
|
||||||
|
|
||||||
|
variable Ar equal 1
|
||||||
|
|
||||||
|
#############
|
||||||
|
#Atom Masses#
|
||||||
|
#############
|
||||||
|
|
||||||
|
mass ${Ar} 39.903
|
||||||
|
|
||||||
|
###########################
|
||||||
|
#Pair Potentials - Tersoff#
|
||||||
|
###########################
|
||||||
|
|
||||||
|
pair_style lj/cubic
|
||||||
|
pair_coeff * * 0.0102701 3.42
|
||||||
|
|
||||||
162
examples/gjf/in.argon
Normal file
162
examples/gjf/in.argon
Normal file
@ -0,0 +1,162 @@
|
|||||||
|
###############################mm
|
||||||
|
# Atom style - charge/vdw/bonded#
|
||||||
|
#################################
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
##############################################
|
||||||
|
#Units Metal : eV - ps - angstrom - bar#
|
||||||
|
# Real : kcal/mol - fs - angstrom - atm#
|
||||||
|
##############################################
|
||||||
|
units metal
|
||||||
|
|
||||||
|
############
|
||||||
|
#Run number#
|
||||||
|
############
|
||||||
|
variable run_no equal 0 # is it a restart?
|
||||||
|
variable res_no equal ${run_no}-1 # restart file number
|
||||||
|
|
||||||
|
#######################################
|
||||||
|
#Random Seeds and Domain Decomposition#
|
||||||
|
#######################################
|
||||||
|
variable iseed0 equal 2357
|
||||||
|
variable iseed1 equal 26488
|
||||||
|
variable iseed2 equal 10669
|
||||||
|
processors * * *
|
||||||
|
|
||||||
|
###########
|
||||||
|
#Data File#
|
||||||
|
###########
|
||||||
|
variable inpfile string argon.lmp
|
||||||
|
variable resfile string final_restart.${res_no}
|
||||||
|
variable ff_file string ff-argon.lmp
|
||||||
|
|
||||||
|
##########
|
||||||
|
#Run Type#
|
||||||
|
##########
|
||||||
|
variable minimise equal 0 #Energy Minimization
|
||||||
|
variable md equal 1 #Plain MD
|
||||||
|
|
||||||
|
###############################
|
||||||
|
#Molecular Dynamics Parameters#
|
||||||
|
###############################
|
||||||
|
variable run_no equal 0 # is it a restart?
|
||||||
|
|
||||||
|
variable ens equal 9 # ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres, 7=stoch, 8=gjf)
|
||||||
|
variable ts equal 0.120 # simulation timestep (time units)
|
||||||
|
variable nequil equal 0 # number of equilibration steps
|
||||||
|
variable nsteps equal 200000 # number of MD steps
|
||||||
|
#variable nsteps equal 20 # number of MD steps
|
||||||
|
|
||||||
|
variable temp_s equal 10 # starting temperature
|
||||||
|
variable temp_f equal 10 # final simulation temperature
|
||||||
|
variable trel equal 1 # thermostat relaxation time
|
||||||
|
variable tscale equal 1 # thermostat relaxation freq - vel rescaling only
|
||||||
|
variable deltat equal 1 # maximum temperature change - vel rescaling only
|
||||||
|
|
||||||
|
variable npttype string iso # type of NPT (iso, aniso, tri, z...)
|
||||||
|
variable pres equal 1.01325 # pressure (NPT runs only)
|
||||||
|
variable prel equal 1.0 # barostat relaxation time
|
||||||
|
|
||||||
|
neighbor 1 bin
|
||||||
|
|
||||||
|
###################
|
||||||
|
#Output Parameters#
|
||||||
|
###################
|
||||||
|
variable ntraj equal 1000 # trajectory output frequency - all system
|
||||||
|
variable ntraj_s equal -100 # trajectory output frequency - solute only
|
||||||
|
variable nthermo equal 200 # thermodynamic data output frequency
|
||||||
|
|
||||||
|
################################
|
||||||
|
#Energy Minimization Parameters#
|
||||||
|
################################
|
||||||
|
variable mtraj equal 1 # trajectory output frequency - all system
|
||||||
|
variable etol equal 1e-5 # % change in energy
|
||||||
|
variable ftol equal 1e-5 # max force threshold (force units)
|
||||||
|
variable maxiter equal 10000 # max # of iterations
|
||||||
|
|
||||||
|
########################
|
||||||
|
#3D Periodic Simulation#
|
||||||
|
########################
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
#############################
|
||||||
|
#Reading the input structure#
|
||||||
|
#############################
|
||||||
|
if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
|
||||||
|
|
||||||
|
#############
|
||||||
|
#Force Field#
|
||||||
|
#############
|
||||||
|
include ${ff_file}
|
||||||
|
|
||||||
|
######################
|
||||||
|
#Thermodynamic Output#
|
||||||
|
######################
|
||||||
|
variable str_basic string 'step time pe temp press'
|
||||||
|
|
||||||
|
#MD ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)
|
||||||
|
variable str_ens string ' '
|
||||||
|
if "${ens} == 0" then "variable str_ens string 'etotal'"
|
||||||
|
if "${ens} == 2" then "variable str_ens string 'vol pxx pyy pzz cella cellb cellc cellakpha cellbeta cellgamma'"
|
||||||
|
|
||||||
|
#Variable for a gulp friend output
|
||||||
|
if "${ens} >= 0" then "thermo_style custom time temp pe etotal press vol cpu" &
|
||||||
|
"thermo ${nthermo}" &
|
||||||
|
"thermo_modify flush yes"
|
||||||
|
|
||||||
|
#####################
|
||||||
|
#Energy Minimization#
|
||||||
|
#####################
|
||||||
|
if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
|
||||||
|
print "Doing CG minimisation"
|
||||||
|
dump mdcd all dcd ${mtraj} min.dcd
|
||||||
|
dump_modify mdcd unwrap yes
|
||||||
|
min_style cg
|
||||||
|
min_modify line quadratic
|
||||||
|
minimize ${etol} ${ftol} ${maxiter} ${maxiter}
|
||||||
|
reset_timestep 0
|
||||||
|
undump mdcd
|
||||||
|
label end_minimise
|
||||||
|
|
||||||
|
################
|
||||||
|
#Timestep in ps#
|
||||||
|
################
|
||||||
|
timestep ${ts}
|
||||||
|
|
||||||
|
##############
|
||||||
|
#Restart file#
|
||||||
|
##############
|
||||||
|
restart 100000 restart.1 restart.2
|
||||||
|
|
||||||
|
###################
|
||||||
|
#Trajectory output#
|
||||||
|
###################
|
||||||
|
#dump xyz all atom 1000 silicon.lammpstrj
|
||||||
|
|
||||||
|
if "${ntraj} > 0" then &
|
||||||
|
"dump 1 all dcd ${ntraj} trajectory.${run_no}.dcd" &
|
||||||
|
"dump_modify 1 unwrap yes"
|
||||||
|
|
||||||
|
fix mom all momentum 1 linear 1 1 1
|
||||||
|
|
||||||
|
###############################################################
|
||||||
|
#Ensembles (0=nve,1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)#
|
||||||
|
###############################################################
|
||||||
|
if "${md} > 0" then 'print "Setting up the ensembles"' &
|
||||||
|
'if "${run_no} == 0" then "velocity all create ${temp_s} ${iseed0} mom yes dist gaussian"' &
|
||||||
|
'if "${ens} == 0" then "fix nve all nve"' &
|
||||||
|
'if "${ens} == 1" then "fix nvt all nvt temp ${temp_s} ${temp_f} ${trel} tchain 5"' &
|
||||||
|
'if "${ens} == 2" then "fix npt all npt temp ${temp_s} ${temp_f} ${trel} ${npttype} ${pres} ${pres} ${prel} tchain 5 pchain 5 mtk yes"' &
|
||||||
|
'if "${ens} == 3" then "fix nve all nve" "fix ber all temp/berendsen ${temp_s} ${temp_f} ${trel}"' &
|
||||||
|
'if "${ens} == 4" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} tally yes zero yes"' &
|
||||||
|
'if "${ens} == 5" then "fix nve all nve" "fix stoch all temp/csvr ${temp_s} ${temp_f} ${trel} ${iseed1}"' &
|
||||||
|
'if "${ens} == 6" then "fix nve all nve" "fix stoch all temp/csld ${temp_s} ${temp_f} ${trel} ${iseed1}"' &
|
||||||
|
'if "${ens} == 7" then "fix nve all nve" "fix vres all temp/rescale ${tscale} ${temp_s} ${temp_f} ${tmin} ${tmax}"' &
|
||||||
|
'if "${ens} == 8" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes"' &
|
||||||
|
'if "${ens} == 9" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes halfstep yes"'
|
||||||
|
|
||||||
|
if "${md} > 0" then "print 'Doing Molecular dynamics'" &
|
||||||
|
"run ${nsteps}" &
|
||||||
|
"write_restart final_restart.${run_no}"
|
||||||
|
|
||||||
|
|
||||||
249
examples/gjf/out.argon
Normal file
249
examples/gjf/out.argon
Normal file
@ -0,0 +1,249 @@
|
|||||||
|
LAMMPS (1 Feb 2019)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
864 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
|
||||||
|
Setting up the ensembles
|
||||||
|
WARNING: Careful, tally is untested (src/fix_langevin.cpp:145)
|
||||||
|
WARNING: Careful, tally is untested (src/fix_langevin.cpp:145)
|
||||||
|
WARNING: Careful, tally is untested (src/fix_langevin.cpp:145)
|
||||||
|
WARNING: Careful, tally is untested (src/fix_langevin.cpp:145)
|
||||||
|
Doing Molecular dynamics
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 6.94072
|
||||||
|
ghost atom cutoff = 6.94072
|
||||||
|
binsize = 3.47036, bins = 10 10 10
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cubic, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : metal
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.12
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.847 | 6.847 | 6.847 Mbytes
|
||||||
|
Time Temp PotEng TotEng Press Volume CPU
|
||||||
|
0 10 -56.207655 -55.09214 33.340921 33218.561 0
|
||||||
|
24 10.156356 -55.092888 -53.959932 339.40964 33218.561 0.082175482
|
||||||
|
48 9.6121006 -55.07262 -54.000376 344.56765 33218.561 0.19529325
|
||||||
|
72 9.8187467 -55.16687 -54.071574 318.85979 33218.561 0.29643488
|
||||||
|
96 9.5421385 -55.151229 -54.086789 322.8842 33218.561 0.38801357
|
||||||
|
120 10.295035 -55.12919 -53.980763 332.00171 33218.561 0.47607262
|
||||||
|
144 10.331608 -55.09907 -53.946563 339.28896 33218.561 0.57389224
|
||||||
|
168 10.154698 -55.058246 -53.925475 349.03253 33218.561 0.65481471
|
||||||
|
192 9.858198 -55.127583 -54.027886 330.09298 33218.561 0.74437734
|
||||||
|
216 9.6658918 -55.10812 -54.029875 334.28383 33218.561 0.8278495
|
||||||
|
240 9.6801591 -55.102386 -54.02255 336.27242 33218.561 0.91167379
|
||||||
|
264 10.685658 -55.046238 -53.854237 355.0448 33218.561 1.0023789
|
||||||
|
288 10.387727 -55.08427 -53.925504 343.87247 33218.561 1.0960371
|
||||||
|
312 10.231132 -55.120428 -53.97913 333.22463 33218.561 1.2382998
|
||||||
|
336 10.20896 -55.075142 -53.936317 344.88438 33218.561 1.3420489
|
||||||
|
360 9.7876538 -55.165008 -54.07318 319.14962 33218.561 1.42782
|
||||||
|
384 9.9872551 -55.13881 -54.024717 327.82471 33218.561 1.5417666
|
||||||
|
408 9.5362734 -55.063733 -53.999947 346.50545 33218.561 1.6328366
|
||||||
|
432 10.262638 -55.126608 -53.981796 332.16342 33218.561 1.7242996
|
||||||
|
456 9.9228239 -55.122119 -54.015214 332.26261 33218.561 1.8124888
|
||||||
|
480 9.7026324 -55.17057 -54.088227 317.84818 33218.561 1.900233
|
||||||
|
504 10.028762 -55.082465 -53.963741 343.04257 33218.561 1.989605
|
||||||
|
528 9.8227851 -55.121222 -54.025476 332.42857 33218.561 2.0708802
|
||||||
|
552 10.208672 -55.100242 -53.961449 338.68109 33218.561 2.1527217
|
||||||
|
576 10.180849 -55.124065 -53.988376 331.29516 33218.561 2.238126
|
||||||
|
600 9.6467252 -55.119533 -54.043427 332.43109 33218.561 2.323443
|
||||||
|
624 10.041885 -55.173802 -54.053614 318.48579 33218.561 2.4046151
|
||||||
|
648 10.151597 -55.111725 -53.979299 334.66227 33218.561 2.4902161
|
||||||
|
672 9.7719111 -55.060111 -53.970039 348.55249 33218.561 2.5800372
|
||||||
|
696 10.476688 -55.088109 -53.919419 342.94922 33218.561 2.6731395
|
||||||
|
720 10.517805 -55.113604 -53.940327 335.47342 33218.561 2.760651
|
||||||
|
744 10.006466 -55.045085 -53.928848 353.53813 33218.561 2.8537894
|
||||||
|
768 10.201492 -55.081598 -53.943606 343.3206 33218.561 2.9404115
|
||||||
|
792 10.117738 -55.077806 -53.949157 345.31093 33218.561 3.030765
|
||||||
|
816 10.362288 -55.11635 -53.960421 333.9045 33218.561 3.1177356
|
||||||
|
840 10.204164 -55.097619 -53.959329 338.82717 33218.561 3.2091886
|
||||||
|
864 10.147722 -55.101372 -53.969378 338.19682 33218.561 3.3003742
|
||||||
|
888 9.9265037 -55.111394 -54.004077 334.08116 33218.561 3.395341
|
||||||
|
912 10.206403 -55.132181 -53.993642 328.89904 33218.561 3.4882881
|
||||||
|
936 10.28639 -55.093317 -53.945855 340.61244 33218.561 3.5764735
|
||||||
|
960 9.8028822 -55.078802 -53.985276 343.5904 33218.561 3.7056267
|
||||||
|
984 10.492755 -55.121321 -53.950839 334.62697 33218.561 3.8055611
|
||||||
|
1008 10.621569 -55.088588 -53.903736 343.33166 33218.561 3.9144807
|
||||||
|
1032 10.006729 -55.113459 -53.997193 334.43025 33218.561 4.0189888
|
||||||
|
1056 10.099853 -55.068035 -53.941381 347.42158 33218.561 4.1391664
|
||||||
|
1080 10.254232 -55.066685 -53.92281 347.15777 33218.561 4.2443953
|
||||||
|
1104 9.9495142 -55.13686 -54.026977 327.63107 33218.561 4.3368342
|
||||||
|
1128 10.377108 -55.08846 -53.930878 344.13083 33218.561 4.4287748
|
||||||
|
1152 10.036981 -55.114643 -53.995003 334.88053 33218.561 4.526868
|
||||||
|
1176 10.144779 -55.097125 -53.965459 339.698 33218.561 4.6614049
|
||||||
|
1200 10.075844 -55.14695 -54.022974 326.05911 33218.561 4.799835
|
||||||
|
1224 10.183695 -55.121716 -53.98571 332.75772 33218.561 4.8908897
|
||||||
|
1248 10.581369 -55.027954 -53.847587 359.06251 33218.561 4.9839788
|
||||||
|
1272 10.158269 -55.105173 -53.972003 337.52964 33218.561 5.0918646
|
||||||
|
1296 9.8776072 -55.064085 -53.962223 347.15648 33218.561 5.2291209
|
||||||
|
1320 10.38161 -55.118366 -53.960282 335.17767 33218.561 5.3570446
|
||||||
|
1344 9.9528146 -55.141937 -54.031685 326.27117 33218.561 5.4584705
|
||||||
|
1368 9.8024326 -55.117808 -54.024332 332.99835 33218.561 5.5557818
|
||||||
|
1392 10.35447 -55.110235 -53.955179 336.80412 33218.561 5.6467392
|
||||||
|
1416 10.199061 -55.105641 -53.96792 337.36785 33218.561 5.7476527
|
||||||
|
1440 9.6868779 -55.087316 -54.00673 340.9166 33218.561 5.8432207
|
||||||
|
1464 10.093238 -55.049436 -53.92352 352.27563 33218.561 5.9471521
|
||||||
|
1488 9.7578808 -55.123935 -54.035429 329.93926 33218.561 6.0495014
|
||||||
|
1512 10.099979 -55.205426 -54.078758 309.26166 33218.561 6.1612976
|
||||||
|
1536 10.172944 -55.087106 -53.952299 342.93395 33218.561 6.2506202
|
||||||
|
1560 10.51771 -55.107635 -53.934369 340.1967 33218.561 6.3379856
|
||||||
|
1584 10.044994 -55.101362 -53.980828 339.03163 33218.561 6.4362567
|
||||||
|
1608 9.624758 -55.146246 -54.07259 324.32486 33218.561 6.5385845
|
||||||
|
1632 9.9135215 -55.097278 -53.99141 338.69162 33218.561 6.6452786
|
||||||
|
1656 9.863681 -55.070523 -53.970214 345.84608 33218.561 6.7518212
|
||||||
|
1680 10.138513 -55.127065 -53.996099 330.40757 33218.561 6.8775188
|
||||||
|
1704 10.382237 -55.070572 -53.912417 347.074 33218.561 7.0126448
|
||||||
|
1728 10.72487 -55.081147 -53.884771 345.83623 33218.561 7.1384216
|
||||||
|
1752 9.829431 -55.131041 -54.034553 328.57652 33218.561 7.2616419
|
||||||
|
1776 9.9135662 -55.100556 -53.994682 336.52238 33218.561 7.4193201
|
||||||
|
1800 10.41873 -55.097116 -53.934891 340.24798 33218.561 7.5570544
|
||||||
|
1824 10.151782 -55.03231 -53.899864 357.3654 33218.561 7.6872905
|
||||||
|
1848 10.42307 -55.043808 -53.881099 355.71677 33218.561 7.7933885
|
||||||
|
1872 10.276862 -55.085016 -53.938616 344.46273 33218.561 7.8887472
|
||||||
|
1896 9.7681373 -55.146507 -54.056857 324.84323 33218.561 7.9977923
|
||||||
|
1920 9.6624824 -55.103214 -54.025349 336.06397 33218.561 8.090235
|
||||||
|
1944 10.153504 -55.049175 -53.916536 352.36339 33218.561 8.1923703
|
||||||
|
1968 10.191954 -55.098741 -53.961813 338.8667 33218.561 8.3320906
|
||||||
|
1992 9.92167 -55.117079 -54.010302 332.96497 33218.561 8.4774437
|
||||||
|
2016 9.5737281 -55.091141 -54.023178 339.41837 33218.561 8.6149527
|
||||||
|
2040 10.600908 -55.092717 -53.91017 342.71852 33218.561 8.7639523
|
||||||
|
2064 9.9214513 -55.099904 -53.993151 337.46799 33218.561 8.898087
|
||||||
|
2088 9.9256258 -55.082224 -53.975005 342.85042 33218.561 9.0130784
|
||||||
|
2112 10.345379 -55.112923 -53.95888 335.81471 33218.561 9.1422766
|
||||||
|
2136 9.8876649 -55.079254 -53.97627 343.05764 33218.561 9.2885707
|
||||||
|
2160 10.04492 -55.074876 -53.95435 344.82419 33218.561 9.3876103
|
||||||
|
2184 10.028705 -55.063961 -53.945244 347.70549 33218.561 9.500967
|
||||||
|
2208 10.412572 -55.136316 -53.974778 329.8188 33218.561 9.5900362
|
||||||
|
2232 10.404205 -55.09913 -53.938525 339.77542 33218.561 9.7048353
|
||||||
|
2256 9.5694135 -55.139021 -54.071538 326.37473 33218.561 9.8045958
|
||||||
|
2280 10.244745 -55.134529 -53.991713 329.19392 33218.561 9.8968908
|
||||||
|
2304 9.9129922 -55.116192 -54.010382 333.14326 33218.561 9.9818651
|
||||||
|
2328 10.167027 -55.08241 -53.948263 343.08135 33218.561 10.068683
|
||||||
|
2352 10.262045 -55.144327 -53.999581 327.40876 33218.561 10.155937
|
||||||
|
2376 10.520934 -55.073147 -53.899521 347.6998 33218.561 10.246316
|
||||||
|
2400 9.9628692 -55.122001 -54.010628 331.25369 33218.561 10.336833
|
||||||
|
2424 10.565531 -55.157113 -53.978512 325.14897 33218.561 10.452039
|
||||||
|
2448 10.03709 -55.096409 -53.976756 338.29607 33218.561 10.537936
|
||||||
|
2472 9.384311 -55.141821 -54.094987 324.23247 33218.561 10.628689
|
||||||
|
2496 9.8019362 -55.105685 -54.012264 335.97239 33218.561 10.717287
|
||||||
|
2520 10.31114 -55.078831 -53.928608 345.42395 33218.561 10.818756
|
||||||
|
2544 10.407237 -55.148382 -53.987439 325.94421 33218.561 10.910801
|
||||||
|
2568 10.257967 -55.041348 -53.897056 355.73261 33218.561 11.004221
|
||||||
|
2592 9.8425807 -55.139428 -54.041474 328.28096 33218.561 11.101295
|
||||||
|
2616 10.140697 -55.100238 -53.969028 338.76319 33218.561 11.192211
|
||||||
|
2640 9.7102818 -55.136288 -54.053091 326.7053 33218.561 11.280277
|
||||||
|
2664 10.120372 -55.128779 -53.999836 330.71707 33218.561 11.369001
|
||||||
|
2688 10.232537 -55.120614 -53.979159 333.35087 33218.561 11.464652
|
||||||
|
2712 10.032526 -55.094761 -53.975618 339.97984 33218.561 11.559387
|
||||||
|
2736 9.8791 -55.121998 -54.01997 332.32556 33218.561 11.649679
|
||||||
|
2760 9.891483 -55.120919 -54.017509 331.32614 33218.561 11.742604
|
||||||
|
2784 10.201053 -55.165525 -54.027582 320.39272 33218.561 11.85274
|
||||||
|
2808 10.238648 -55.096449 -53.954312 340.06316 33218.561 11.939782
|
||||||
|
2832 9.8692851 -55.068632 -53.967699 346.77535 33218.561 12.036655
|
||||||
|
2856 10.179976 -55.128413 -53.992822 331.5662 33218.561 12.123227
|
||||||
|
2880 9.7656315 -55.1468 -54.057429 324.02612 33218.561 12.213117
|
||||||
|
2904 9.7991628 -55.049191 -53.95608 352.45738 33218.561 12.326761
|
||||||
|
2928 10.581767 -55.093293 -53.912881 341.37292 33218.561 12.417633
|
||||||
|
2952 10.546144 -55.07452 -53.898081 347.02025 33218.561 12.52701
|
||||||
|
2976 9.8306008 -55.14762 -54.051002 323.45715 33218.561 12.633522
|
||||||
|
3000 10.033532 -55.076433 -53.957178 345.36812 33218.561 12.72627
|
||||||
|
3024 10.046266 -55.085775 -53.965099 342.47786 33218.561 12.816242
|
||||||
|
3048 10.176777 -55.133013 -53.997778 329.04144 33218.561 12.903175
|
||||||
|
3072 9.9778064 -55.143787 -54.030748 326.75284 33218.561 13.014329
|
||||||
|
3096 10.516223 -55.110144 -53.937043 336.802 33218.561 13.104673
|
||||||
|
3120 9.6561157 -55.138699 -54.061544 325.6652 33218.561 13.207371
|
||||||
|
3144 10.237043 -55.060968 -53.91901 349.44011 33218.561 13.303442
|
||||||
|
3168 9.9704264 -55.123073 -54.010857 332.19725 33218.561 13.391877
|
||||||
|
3192 10.493307 -55.144402 -53.973858 327.15485 33218.561 13.482857
|
||||||
|
3216 10.022171 -55.141782 -54.023794 326.08249 33218.561 13.574484
|
||||||
|
3240 9.6957248 -55.137865 -54.056292 326.04858 33218.561 13.671408
|
||||||
|
3264 9.9685299 -55.124301 -54.012297 331.9015 33218.561 13.760186
|
||||||
|
3288 10.413707 -55.153604 -53.99194 324.32939 33218.561 13.877604
|
||||||
|
3312 10.022953 -55.103422 -53.985346 337.52066 33218.561 13.977562
|
||||||
|
3336 10.044478 -55.110297 -53.98982 334.48379 33218.561 14.065563
|
||||||
|
3360 9.8593734 -55.130623 -54.030795 327.71748 33218.561 14.15952
|
||||||
|
3384 9.9269422 -55.107979 -54.000613 335.18173 33218.561 14.258064
|
||||||
|
3408 10.288049 -55.092276 -53.944629 340.71484 33218.561 14.36211
|
||||||
|
3432 9.9702156 -55.08732 -53.975128 341.72171 33218.561 14.452123
|
||||||
|
3456 10.246178 -55.091669 -53.948692 341.62844 33218.561 14.555775
|
||||||
|
3480 10.559292 -55.086917 -53.909012 343.70626 33218.561 14.645718
|
||||||
|
3504 10.652207 -55.050897 -53.862628 354.46979 33218.561 14.797422
|
||||||
|
3528 9.9835266 -55.0557 -53.942023 350.74747 33218.561 14.895716
|
||||||
|
3552 10.240934 -55.123217 -53.980825 332.26434 33218.561 15.023796
|
||||||
|
3576 10.406519 -55.093536 -53.932674 341.54029 33218.561 15.203252
|
||||||
|
3600 10.406733 -55.095168 -53.934282 341.22192 33218.561 15.303986
|
||||||
|
3624 9.9877484 -55.154231 -54.040083 323.55633 33218.561 15.398883
|
||||||
|
3648 10.391829 -55.110208 -53.950984 337.09219 33218.561 15.49042
|
||||||
|
3672 10.368995 -55.069591 -53.912914 346.82649 33218.561 15.582259
|
||||||
|
3696 10.362939 -55.109012 -53.953011 337.32216 33218.561 15.679316
|
||||||
|
3720 10.465254 -55.136214 -53.968799 331.22288 33218.561 15.773303
|
||||||
|
3744 9.8238226 -55.10114 -54.005278 338.12616 33218.561 15.86905
|
||||||
|
3768 10.205504 -55.101263 -53.962824 339.04196 33218.561 15.960072
|
||||||
|
3792 9.9589987 -55.118883 -54.007942 332.84318 33218.561 16.047055
|
||||||
|
3816 10.253382 -55.117513 -53.973732 334.42101 33218.561 16.148412
|
||||||
|
3840 10.262393 -55.069549 -53.924764 349.084 33218.561 16.235391
|
||||||
|
3864 9.7367167 -55.078288 -53.992142 342.48207 33218.561 16.329112
|
||||||
|
3888 10.171202 -55.134701 -54.000088 329.5847 33218.561 16.415353
|
||||||
|
3912 10.01925 -55.145139 -54.027477 326.65074 33218.561 16.526334
|
||||||
|
3936 10.053638 -55.038151 -53.916653 355.74893 33218.561 16.618524
|
||||||
|
3960 10.044055 -55.058382 -53.937953 349.01834 33218.561 16.712577
|
||||||
|
3984 10.382422 -55.099216 -53.941041 339.28099 33218.561 16.79941
|
||||||
|
4008 9.97927 -55.09284 -53.979637 339.07225 33218.561 16.904198
|
||||||
|
4032 9.6782319 -55.126143 -54.046522 329.0201 33218.561 16.991454
|
||||||
|
4056 9.6593809 -55.123677 -54.046159 329.89833 33218.561 17.097172
|
||||||
|
4080 10.442896 -55.141149 -53.976229 327.9899 33218.561 17.189364
|
||||||
|
4104 9.9571109 -55.08588 -53.975149 341.3746 33218.561 17.294147
|
||||||
|
4128 10.44943 -55.087946 -53.922296 343.09435 33218.561 17.387357
|
||||||
|
4152 10.040581 -55.171939 -54.051897 317.85348 33218.561 17.500905
|
||||||
|
4176 10.089442 -55.128713 -54.00322 330.29121 33218.561 17.588891
|
||||||
|
4200 10.316156 -55.123219 -53.972436 333.59382 33218.561 17.679254
|
||||||
|
4224 10.177245 -55.095671 -53.960384 339.34498 33218.561 17.770569
|
||||||
|
4248 9.7129183 -55.135335 -54.051844 328.25125 33218.561 17.857728
|
||||||
|
4272 10.231838 -55.099554 -53.958177 339.64015 33218.561 17.944226
|
||||||
|
4296 9.9737677 -55.117885 -54.005297 333.07248 33218.561 18.034105
|
||||||
|
4320 10.004955 -55.116155 -54.000088 333.52271 33218.561 18.129644
|
||||||
|
4344 9.5938901 -55.133824 -54.063612 327.84171 33218.561 18.215476
|
||||||
|
4368 9.8954562 -55.131603 -54.02775 329.0813 33218.561 18.306539
|
||||||
|
4392 10.439732 -55.100379 -53.935812 339.81679 33218.561 18.395651
|
||||||
|
4416 9.934513 -55.08449 -53.97628 341.74441 33218.561 18.484506
|
||||||
|
4440 10.025998 -55.136771 -54.018356 327.73718 33218.561 18.593946
|
||||||
|
4464 9.9304451 -55.101817 -53.994061 338.1801 33218.561 18.684011
|
||||||
|
4488 10.344371 -55.085856 -53.931926 342.91721 33218.561 18.782399
|
||||||
|
4512 10.033193 -55.091778 -53.972561 339.85728 33218.561 18.879666
|
||||||
|
4536 9.2361614 -55.169375 -54.139067 316.67597 33218.561 18.983667
|
||||||
|
4560 9.5786289 -55.179976 -54.111465 314.76415 33218.561 19.079009
|
||||||
|
4584 10.071651 -55.107218 -53.98371 336.10364 33218.561 19.163975
|
||||||
|
4608 9.9873098 -55.109348 -53.995249 336.03665 33218.561 19.25635
|
||||||
|
4632 10.143888 -55.119423 -53.987857 333.74978 33218.561 19.346658
|
||||||
|
4656 9.7506264 -55.114772 -54.027075 332.98271 33218.561 19.435425
|
||||||
|
4680 9.9616769 -55.096054 -53.984814 339.20499 33218.561 19.55562
|
||||||
|
4704 10.271313 -55.074522 -53.928742 345.87397 33218.561 19.642652
|
||||||
|
4728 9.9172336 -55.098805 -53.992523 338.06318 33218.561 19.734557
|
||||||
|
4752 9.9556222 -55.12128 -54.010716 332.66408 33218.561 19.83859
|
||||||
|
4776 10.197593 -55.095293 -53.957736 339.50067 33218.561 19.947471
|
||||||
|
4800 10.145085 -55.108467 -53.976768 336.05115 33218.561 20.044183
|
||||||
|
4824 10.205523 -55.147376 -54.008934 325.56559 33218.561 20.144393
|
||||||
|
4848 9.8900281 -55.121598 -54.01835 331.17401 33218.561 20.243197
|
||||||
|
4872 10.03655 -55.100936 -53.981343 337.6777 33218.561 20.336043
|
||||||
|
4896 9.8120635 -55.087507 -53.992957 341.42438 33218.561 20.425498
|
||||||
|
4920 10.615354 -55.093335 -53.909176 342.30776 33218.561 20.519318
|
||||||
|
4944 10.374366 -55.06455 -53.907274 351.10607 33218.561 20.612312
|
||||||
|
4968 10.677474 -55.147807 -53.956718 327.85703 33218.561 20.719371
|
||||||
|
4992 10.558882 -55.145253 -53.967393 327.427 33218.561 20.818726
|
||||||
|
5016 9.4097946 -55.150835 -54.101158 321.62641 33218.561 20.914472
|
||||||
BIN
examples/gjf/trajectory.0.dcd
Normal file
BIN
examples/gjf/trajectory.0.dcd
Normal file
Binary file not shown.
@ -98,6 +98,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
oflag = 0;
|
oflag = 0;
|
||||||
tallyflag = 0;
|
tallyflag = 0;
|
||||||
zeroflag = 0;
|
zeroflag = 0;
|
||||||
|
hsflag = 0;
|
||||||
|
|
||||||
int iarg = 7;
|
int iarg = 7;
|
||||||
while (iarg < narg) {
|
while (iarg < narg) {
|
||||||
@ -138,6 +139,14 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
else if (strcmp(arg[iarg+1],"yes") == 0) zeroflag = 1;
|
else if (strcmp(arg[iarg+1],"yes") == 0) zeroflag = 1;
|
||||||
else error->all(FLERR,"Illegal fix langevin command");
|
else error->all(FLERR,"Illegal fix langevin command");
|
||||||
iarg += 2;
|
iarg += 2;
|
||||||
|
} else if (strcmp(arg[iarg],"halfstep") == 0) {
|
||||||
|
if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command");
|
||||||
|
if (gjfflag == 0) error->all(FLERR,"GJF must be set");
|
||||||
|
if (tallyflag == 0) error->warning(FLERR,"Careful, tally is untested");
|
||||||
|
if (strcmp(arg[iarg+1],"no") == 0) hsflag = 0;
|
||||||
|
else if (strcmp(arg[iarg+1],"yes") == 0) hsflag = 1;
|
||||||
|
else error->all(FLERR,"Illegal fix langevin command");
|
||||||
|
iarg += 2;
|
||||||
} else error->all(FLERR,"Illegal fix langevin command");
|
} else error->all(FLERR,"Illegal fix langevin command");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -155,6 +164,8 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
flangevin = NULL;
|
flangevin = NULL;
|
||||||
flangevin_allocated = 0;
|
flangevin_allocated = 0;
|
||||||
franprev = NULL;
|
franprev = NULL;
|
||||||
|
wildcard = NULL;
|
||||||
|
lv = NULL;
|
||||||
tforce = NULL;
|
tforce = NULL;
|
||||||
maxatom1 = maxatom2 = 0;
|
maxatom1 = maxatom2 = 0;
|
||||||
|
|
||||||
@ -163,6 +174,12 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// no need to set peratom_flag, b/c data is for internal use only
|
// no need to set peratom_flag, b/c data is for internal use only
|
||||||
|
|
||||||
if (gjfflag) {
|
if (gjfflag) {
|
||||||
|
int mem = 6*atom->nmax*sizeof(double);
|
||||||
|
if (hsflag) mem += 3*atom->nmax*sizeof(double);
|
||||||
|
|
||||||
|
comm->maxexchange_fix = MAX(comm->maxexchange_fix, 0);
|
||||||
|
comm->maxexchange_fix += MAX(1000, mem);
|
||||||
|
|
||||||
nvalues = 3;
|
nvalues = 3;
|
||||||
grow_arrays(atom->nmax);
|
grow_arrays(atom->nmax);
|
||||||
atom->add_callback(0);
|
atom->add_callback(0);
|
||||||
@ -174,6 +191,14 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
franprev[i][0] = 0.0;
|
franprev[i][0] = 0.0;
|
||||||
franprev[i][1] = 0.0;
|
franprev[i][1] = 0.0;
|
||||||
franprev[i][2] = 0.0;
|
franprev[i][2] = 0.0;
|
||||||
|
wildcard[i][0] = 0.0;
|
||||||
|
wildcard[i][1] = 0.0;
|
||||||
|
wildcard[i][2] = 0.0;
|
||||||
|
if (hsflag) {
|
||||||
|
lv[i][0] = 0.0;
|
||||||
|
lv[i][1] = 0.0;
|
||||||
|
lv[i][2] = 0.0;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -194,6 +219,8 @@ FixLangevin::~FixLangevin()
|
|||||||
|
|
||||||
if (gjfflag) {
|
if (gjfflag) {
|
||||||
memory->destroy(franprev);
|
memory->destroy(franprev);
|
||||||
|
memory->destroy(wildcard);
|
||||||
|
if (hsflag) memory->destroy(lv);
|
||||||
atom->delete_callback(id,0);
|
atom->delete_callback(id,0);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -203,6 +230,8 @@ FixLangevin::~FixLangevin()
|
|||||||
int FixLangevin::setmask()
|
int FixLangevin::setmask()
|
||||||
{
|
{
|
||||||
int mask = 0;
|
int mask = 0;
|
||||||
|
//if (gjfflag) mask |= INITIAL_INTEGRATE;
|
||||||
|
if (gjfflag) mask |= POST_INTEGRATE;
|
||||||
mask |= POST_FORCE;
|
mask |= POST_FORCE;
|
||||||
mask |= POST_FORCE_RESPA;
|
mask |= POST_FORCE_RESPA;
|
||||||
mask |= END_OF_STEP;
|
mask |= END_OF_STEP;
|
||||||
@ -258,13 +287,11 @@ void FixLangevin::init()
|
|||||||
error->one(FLERR,"Fix langevin angmom requires extended particles");
|
error->one(FLERR,"Fix langevin angmom requires extended particles");
|
||||||
}
|
}
|
||||||
|
|
||||||
// set force prefactors
|
|
||||||
|
|
||||||
if (!atom->rmass) {
|
if (!atom->rmass) {
|
||||||
for (int i = 1; i <= atom->ntypes; i++) {
|
for (int i = 1; i <= atom->ntypes; i++) {
|
||||||
gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
|
gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
|
||||||
gfactor2[i] = sqrt(atom->mass[i]) *
|
gfactor2[i] = sqrt(atom->mass[i]) *
|
||||||
sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
|
sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) /
|
||||||
force->ftm2v;
|
force->ftm2v;
|
||||||
gfactor1[i] *= 1.0/ratio[i];
|
gfactor1[i] *= 1.0/ratio[i];
|
||||||
gfactor2[i] *= 1.0/sqrt(ratio[i]);
|
gfactor2[i] *= 1.0/sqrt(ratio[i]);
|
||||||
@ -277,7 +304,7 @@ void FixLangevin::init()
|
|||||||
if (strstr(update->integrate_style,"respa"))
|
if (strstr(update->integrate_style,"respa"))
|
||||||
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||||
|
|
||||||
if (gjfflag) gjffac = 1.0/(1.0+update->dt/2.0/t_period);
|
if (gjfflag) gjffac = 1.0/sqrt(1.0+update->dt/2.0/t_period);
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -292,6 +319,94 @@ void FixLangevin::setup(int vflag)
|
|||||||
post_force_respa(vflag,nlevels_respa-1,0);
|
post_force_respa(vflag,nlevels_respa-1,0);
|
||||||
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
||||||
}
|
}
|
||||||
|
if (gjfflag && hsflag) {
|
||||||
|
|
||||||
|
double dt = update->dt;
|
||||||
|
|
||||||
|
// update v of atoms in group
|
||||||
|
|
||||||
|
double **v = atom->v;
|
||||||
|
double *rmass = atom->rmass;
|
||||||
|
int *type = atom->type;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
double boltz = force->boltz;
|
||||||
|
double mvv2e = force->mvv2e;
|
||||||
|
double ftm2v = force->ftm2v;
|
||||||
|
|
||||||
|
double gamma2;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
if (rmass) {
|
||||||
|
gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||||
|
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
||||||
|
} else {
|
||||||
|
gamma2 = gfactor2[type[i]] * tsqrt;
|
||||||
|
}
|
||||||
|
|
||||||
|
franprev[i][0] = gamma2*random->gaussian();
|
||||||
|
franprev[i][1] = gamma2*random->gaussian();
|
||||||
|
franprev[i][2] = gamma2*random->gaussian();
|
||||||
|
wildcard[i][0] = v[i][0];
|
||||||
|
wildcard[i][1] = v[i][1];
|
||||||
|
wildcard[i][2] = v[i][2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
allow for both per-type and per-atom mass
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixLangevin::post_integrate()
|
||||||
|
{
|
||||||
|
double dtfm;
|
||||||
|
double dt = update->dt;
|
||||||
|
double dtf = 0.5 * dt * force->ftm2v;
|
||||||
|
|
||||||
|
// update v of atoms in group
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double **v = atom->v;
|
||||||
|
double **f = atom->f;
|
||||||
|
double *rmass = atom->rmass;
|
||||||
|
double *mass = atom->mass;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
if (rmass) {
|
||||||
|
for (int i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
dtfm = dtf / rmass[i];
|
||||||
|
x[i][0] += -dt * v[i][0];
|
||||||
|
x[i][1] += -dt * v[i][1];
|
||||||
|
x[i][2] += -dt * v[i][2];
|
||||||
|
v[i][0] = gjffac * (wildcard[i][0] + dtfm * franprev[i][0] + dtfm * f[i][0]);
|
||||||
|
v[i][1] = gjffac * (wildcard[i][1] + dtfm * franprev[i][1] + dtfm * f[i][1]);
|
||||||
|
v[i][2] = gjffac * (wildcard[i][2] + dtfm * franprev[i][2] + dtfm * f[i][2]);
|
||||||
|
x[i][0] += gjffac * dt * v[i][0];
|
||||||
|
x[i][1] += gjffac * dt * v[i][1];
|
||||||
|
x[i][2] += gjffac * dt * v[i][2];
|
||||||
|
}
|
||||||
|
|
||||||
|
} else {
|
||||||
|
for (int i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
dtfm = dtf / mass[type[i]];
|
||||||
|
x[i][0] += -dt * v[i][0];
|
||||||
|
x[i][1] += -dt * v[i][1];
|
||||||
|
x[i][2] += -dt * v[i][2];
|
||||||
|
v[i][0] = gjffac * (wildcard[i][0] + dtfm * franprev[i][0] + dtfm * f[i][0]);
|
||||||
|
v[i][1] = gjffac * (wildcard[i][1] + dtfm * franprev[i][1] + dtfm * f[i][1]);
|
||||||
|
v[i][2] = gjffac * (wildcard[i][2] + dtfm * franprev[i][2] + dtfm * f[i][2]);
|
||||||
|
x[i][0] += gjffac * dt * v[i][0];
|
||||||
|
x[i][1] += gjffac * dt * v[i][1];
|
||||||
|
x[i][2] += gjffac * dt * v[i][2];
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -477,9 +592,8 @@ void FixLangevin::post_force_templated()
|
|||||||
// sum random force over all atoms in group
|
// sum random force over all atoms in group
|
||||||
// subtract sum/count from each atom in group
|
// subtract sum/count from each atom in group
|
||||||
|
|
||||||
double fdrag[3],fran[3],fsum[3],fsumall[3];
|
double fdrag[3],fran[3],fsum[3],fsumall[3], rantemp[3];
|
||||||
bigint count;
|
bigint count;
|
||||||
double fswap;
|
|
||||||
|
|
||||||
double boltz = force->boltz;
|
double boltz = force->boltz;
|
||||||
double dt = update->dt;
|
double dt = update->dt;
|
||||||
@ -513,7 +627,7 @@ void FixLangevin::post_force_templated()
|
|||||||
if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]);
|
if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]);
|
||||||
if (Tp_RMASS) {
|
if (Tp_RMASS) {
|
||||||
gamma1 = -rmass[i] / t_period / ftm2v;
|
gamma1 = -rmass[i] / t_period / ftm2v;
|
||||||
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||||
gamma1 *= 1.0/ratio[type[i]];
|
gamma1 *= 1.0/ratio[type[i]];
|
||||||
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
||||||
} else {
|
} else {
|
||||||
@ -521,9 +635,9 @@ void FixLangevin::post_force_templated()
|
|||||||
gamma2 = gfactor2[type[i]] * tsqrt;
|
gamma2 = gfactor2[type[i]] * tsqrt;
|
||||||
}
|
}
|
||||||
|
|
||||||
fran[0] = gamma2*(random->uniform()-0.5);
|
fran[0] = gamma2*random->gaussian();
|
||||||
fran[1] = gamma2*(random->uniform()-0.5);
|
fran[1] = gamma2*random->gaussian();
|
||||||
fran[2] = gamma2*(random->uniform()-0.5);
|
fran[2] = gamma2*random->gaussian();
|
||||||
|
|
||||||
if (Tp_BIAS) {
|
if (Tp_BIAS) {
|
||||||
temperature->remove_bias(i,v[i]);
|
temperature->remove_bias(i,v[i]);
|
||||||
@ -541,25 +655,20 @@ void FixLangevin::post_force_templated()
|
|||||||
}
|
}
|
||||||
|
|
||||||
if (Tp_GJF) {
|
if (Tp_GJF) {
|
||||||
fswap = 0.5*(fran[0]+franprev[i][0]);
|
wildcard[i][0] = f[i][0];
|
||||||
franprev[i][0] = fran[0];
|
wildcard[i][1] = f[i][1];
|
||||||
fran[0] = fswap;
|
wildcard[i][2] = f[i][2];
|
||||||
fswap = 0.5*(fran[1]+franprev[i][1]);
|
|
||||||
franprev[i][1] = fran[1];
|
|
||||||
fran[1] = fswap;
|
|
||||||
fswap = 0.5*(fran[2]+franprev[i][2]);
|
|
||||||
franprev[i][2] = fran[2];
|
|
||||||
fran[2] = fswap;
|
|
||||||
|
|
||||||
fdrag[0] *= gjffac;
|
rantemp[0] = fran[0];
|
||||||
fdrag[1] *= gjffac;
|
rantemp[1] = fran[1];
|
||||||
fdrag[2] *= gjffac;
|
rantemp[2] = fran[2];
|
||||||
fran[0] *= gjffac;
|
fran[0] = franprev[i][0];
|
||||||
fran[1] *= gjffac;
|
fran[1] = franprev[i][1];
|
||||||
fran[2] *= gjffac;
|
fran[2] = franprev[i][2];
|
||||||
f[i][0] *= gjffac;
|
|
||||||
f[i][1] *= gjffac;
|
fdrag[0] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt;
|
||||||
f[i][2] *= gjffac;
|
fdrag[1] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt;
|
||||||
|
fdrag[2] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt;
|
||||||
}
|
}
|
||||||
|
|
||||||
f[i][0] += fdrag[0] + fran[0];
|
f[i][0] += fdrag[0] + fran[0];
|
||||||
@ -567,6 +676,11 @@ void FixLangevin::post_force_templated()
|
|||||||
f[i][2] += fdrag[2] + fran[2];
|
f[i][2] += fdrag[2] + fran[2];
|
||||||
|
|
||||||
if (Tp_TALLY) {
|
if (Tp_TALLY) {
|
||||||
|
if (Tp_GJF){
|
||||||
|
fdrag[0] = gamma1*gjffac*v[i][0];
|
||||||
|
fdrag[1] = gamma1*gjffac*v[i][1];
|
||||||
|
fdrag[2] = gamma1*gjffac*v[i][2];
|
||||||
|
}
|
||||||
flangevin[i][0] = fdrag[0] + fran[0];
|
flangevin[i][0] = fdrag[0] + fran[0];
|
||||||
flangevin[i][1] = fdrag[1] + fran[1];
|
flangevin[i][1] = fdrag[1] + fran[1];
|
||||||
flangevin[i][2] = fdrag[2] + fran[2];
|
flangevin[i][2] = fdrag[2] + fran[2];
|
||||||
@ -577,6 +691,19 @@ void FixLangevin::post_force_templated()
|
|||||||
fsum[1] += fran[1];
|
fsum[1] += fran[1];
|
||||||
fsum[2] += fran[2];
|
fsum[2] += fran[2];
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (Tp_GJF)
|
||||||
|
{
|
||||||
|
franprev[i][0] = rantemp[0];
|
||||||
|
franprev[i][1] = rantemp[1];
|
||||||
|
franprev[i][2] = rantemp[2];
|
||||||
|
|
||||||
|
if (hsflag){
|
||||||
|
lv[i][0] = v[i][0];
|
||||||
|
lv[i][1] = v[i][1];
|
||||||
|
lv[i][2] = v[i][2];
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -641,9 +768,9 @@ void FixLangevin::compute_target()
|
|||||||
input->variable->compute_atom(tvar,igroup,tforce,1,0);
|
input->variable->compute_atom(tvar,igroup,tforce,1,0);
|
||||||
for (int i = 0; i < nlocal; i++)
|
for (int i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit)
|
if (mask[i] & groupbit)
|
||||||
if (tforce[i] < 0.0)
|
if (tforce[i] < 0.0)
|
||||||
error->one(FLERR,
|
error->one(FLERR,
|
||||||
"Fix langevin variable returned negative temperature");
|
"Fix langevin variable returned negative temperature");
|
||||||
}
|
}
|
||||||
modify->addstep_compute(update->ntimestep + 1);
|
modify->addstep_compute(update->ntimestep + 1);
|
||||||
}
|
}
|
||||||
@ -756,20 +883,41 @@ void FixLangevin::angmom_thermostat()
|
|||||||
|
|
||||||
void FixLangevin::end_of_step()
|
void FixLangevin::end_of_step()
|
||||||
{
|
{
|
||||||
if (!tallyflag) return;
|
if (!tallyflag && !gjfflag) return;
|
||||||
|
|
||||||
double **v = atom->v;
|
double **v = atom->v;
|
||||||
|
double **f = atom->f;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
int nlocal = atom->nlocal;
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
energy_onestep = 0.0;
|
energy_onestep = 0.0;
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; i++)
|
for (int i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit)
|
if (mask[i] & groupbit) {
|
||||||
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
|
if (gjfflag){
|
||||||
flangevin[i][2]*v[i][2];
|
f[i][0] = wildcard[i][0];
|
||||||
|
f[i][1] = wildcard[i][1];
|
||||||
energy += energy_onestep*update->dt;
|
f[i][2] = wildcard[i][2];
|
||||||
|
wildcard[i][0] = v[i][0];
|
||||||
|
wildcard[i][1] = v[i][1];
|
||||||
|
wildcard[i][2] = v[i][2];
|
||||||
|
if (hsflag){
|
||||||
|
v[i][0] = lv[i][0];
|
||||||
|
v[i][1] = lv[i][1];
|
||||||
|
v[i][2] = lv[i][2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (tallyflag && hsflag){
|
||||||
|
energy_onestep += gjffac*(flangevin[i][0] * lv[i][0] +
|
||||||
|
flangevin[i][1] * lv[i][1] + flangevin[i][2] * lv[i][2]);
|
||||||
|
}
|
||||||
|
else if (tallyflag){
|
||||||
|
energy_onestep += flangevin[i][0] * v[i][0] + flangevin[i][1] * v[i][1] +
|
||||||
|
flangevin[i][2] * v[i][2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (tallyflag) {
|
||||||
|
energy += energy_onestep * update->dt;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -869,7 +1017,8 @@ void *FixLangevin::extract(const char *str, int &dim)
|
|||||||
double FixLangevin::memory_usage()
|
double FixLangevin::memory_usage()
|
||||||
{
|
{
|
||||||
double bytes = 0.0;
|
double bytes = 0.0;
|
||||||
if (gjfflag) bytes += atom->nmax*3 * sizeof(double);
|
if (gjfflag) bytes += atom->nmax*3*2 * sizeof(double);
|
||||||
|
if (gjfflag) if (hsflag) bytes += atom->nmax*3 * sizeof(double);
|
||||||
if (tallyflag) bytes += atom->nmax*3 * sizeof(double);
|
if (tallyflag) bytes += atom->nmax*3 * sizeof(double);
|
||||||
if (tforce) bytes += atom->nmax * sizeof(double);
|
if (tforce) bytes += atom->nmax * sizeof(double);
|
||||||
return bytes;
|
return bytes;
|
||||||
@ -882,6 +1031,8 @@ double FixLangevin::memory_usage()
|
|||||||
void FixLangevin::grow_arrays(int nmax)
|
void FixLangevin::grow_arrays(int nmax)
|
||||||
{
|
{
|
||||||
memory->grow(franprev,nmax,3,"fix_langevin:franprev");
|
memory->grow(franprev,nmax,3,"fix_langevin:franprev");
|
||||||
|
memory->grow(wildcard,nmax,3,"fix_langevin:wildcard");
|
||||||
|
if (hsflag) memory->grow(lv,nmax,3,"fix_langevin:lv");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -890,8 +1041,17 @@ void FixLangevin::grow_arrays(int nmax)
|
|||||||
|
|
||||||
void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
|
void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
|
||||||
{
|
{
|
||||||
for (int m = 0; m < nvalues; m++)
|
franprev[j][0] = franprev[i][0];
|
||||||
franprev[j][m] = franprev[i][m];
|
franprev[j][1] = franprev[i][1];
|
||||||
|
franprev[j][2] = franprev[i][2];
|
||||||
|
wildcard[j][0] = wildcard[i][0];
|
||||||
|
wildcard[j][1] = wildcard[i][1];
|
||||||
|
wildcard[j][2] = wildcard[i][2];
|
||||||
|
if (hsflag) {
|
||||||
|
lv[j][0] = lv[i][0];
|
||||||
|
lv[j][1] = lv[i][1];
|
||||||
|
lv[j][2] = lv[i][2];
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -900,8 +1060,19 @@ void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
|
|||||||
|
|
||||||
int FixLangevin::pack_exchange(int i, double *buf)
|
int FixLangevin::pack_exchange(int i, double *buf)
|
||||||
{
|
{
|
||||||
for (int m = 0; m < nvalues; m++) buf[m] = franprev[i][m];
|
int n = 0;
|
||||||
return nvalues;
|
buf[n++] = franprev[i][0];
|
||||||
|
buf[n++] = franprev[i][1];
|
||||||
|
buf[n++] = franprev[i][2];
|
||||||
|
buf[n++] = wildcard[i][0];
|
||||||
|
buf[n++] = wildcard[i][1];
|
||||||
|
buf[n++] = wildcard[i][2];
|
||||||
|
if (hsflag){
|
||||||
|
buf[n++] = lv[i][0];
|
||||||
|
buf[n++] = lv[i][1];
|
||||||
|
buf[n++] = lv[i][2];
|
||||||
|
}
|
||||||
|
return n;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -910,6 +1081,17 @@ int FixLangevin::pack_exchange(int i, double *buf)
|
|||||||
|
|
||||||
int FixLangevin::unpack_exchange(int nlocal, double *buf)
|
int FixLangevin::unpack_exchange(int nlocal, double *buf)
|
||||||
{
|
{
|
||||||
for (int m = 0; m < nvalues; m++) franprev[nlocal][m] = buf[m];
|
int n = 0;
|
||||||
return nvalues;
|
franprev[nlocal][0] = buf[n++];
|
||||||
|
franprev[nlocal][1] = buf[n++];
|
||||||
|
franprev[nlocal][2] = buf[n++];
|
||||||
|
wildcard[nlocal][0] = buf[n++];
|
||||||
|
wildcard[nlocal][1] = buf[n++];
|
||||||
|
wildcard[nlocal][2] = buf[n++];
|
||||||
|
if (hsflag){
|
||||||
|
lv[nlocal][0] = buf[n++];
|
||||||
|
lv[nlocal][1] = buf[n++];
|
||||||
|
lv[nlocal][2] = buf[n++];
|
||||||
|
}
|
||||||
|
return n;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -31,6 +31,8 @@ class FixLangevin : public Fix {
|
|||||||
int setmask();
|
int setmask();
|
||||||
void init();
|
void init();
|
||||||
void setup(int);
|
void setup(int);
|
||||||
|
//virtual void initial_integrate(int);
|
||||||
|
virtual void post_integrate();
|
||||||
virtual void post_force(int);
|
virtual void post_force(int);
|
||||||
void post_force_respa(int, int, int);
|
void post_force_respa(int, int, int);
|
||||||
virtual void end_of_step();
|
virtual void end_of_step();
|
||||||
@ -46,7 +48,7 @@ class FixLangevin : public Fix {
|
|||||||
int unpack_exchange(int, double *);
|
int unpack_exchange(int, double *);
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
int gjfflag,oflag,tallyflag,zeroflag,tbiasflag;
|
int gjfflag,oflag,tallyflag,zeroflag,tbiasflag,hsflag;
|
||||||
int flangevin_allocated;
|
int flangevin_allocated;
|
||||||
double ascale;
|
double ascale;
|
||||||
double t_start,t_stop,t_period,t_target;
|
double t_start,t_stop,t_period,t_target;
|
||||||
@ -63,6 +65,9 @@ class FixLangevin : public Fix {
|
|||||||
double **flangevin;
|
double **flangevin;
|
||||||
double *tforce;
|
double *tforce;
|
||||||
double **franprev;
|
double **franprev;
|
||||||
|
double **lv; //lucas velocity or half-step velocity
|
||||||
|
double **wildcard;
|
||||||
|
|
||||||
int nvalues;
|
int nvalues;
|
||||||
|
|
||||||
char *id_temp;
|
char *id_temp;
|
||||||
|
|||||||
Reference in New Issue
Block a user