update kolmogorov-crespi examples
This commit is contained in:
Axel Kohlmeyer
@ -1,266 +0,0 @@
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info: xyz2data 18:31, Mon 27-02-2017
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256 atoms
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2 atom types
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0.00000000 17.04000000 xlo xhi
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0.00000000 19.67609717 ylo yhi
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-20.00000000 40.00000000 zlo zhi
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Atoms
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1 1 0.00000000 0.00000000 0.00000000
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2 1 1.42000000 0.00000000 0.00000000
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3 2 1.42000000 0.00000000 3.30000000
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4 2 2.84000000 0.00000000 3.30000000
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5 1 2.13000000 1.22975607 0.00000000
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6 1 3.55000000 1.22975607 0.00000000
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7 2 3.55000000 1.22975607 3.30000000
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8 2 4.97000000 1.22975607 3.30000000
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9 1 0.00000000 2.45951215 0.00000000
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10 1 1.42000000 2.45951215 0.00000000
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11 2 1.42000000 2.45951215 3.30000000
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12 2 2.84000000 2.45951215 3.30000000
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13 1 2.13000000 3.68926822 0.00000000
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14 1 3.55000000 3.68926822 0.00000000
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15 2 3.55000000 3.68926822 3.30000000
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16 2 4.97000000 3.68926822 3.30000000
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17 1 0.00000000 4.91902429 0.00000000
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18 1 1.42000000 4.91902429 0.00000000
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19 2 1.42000000 4.91902429 3.30000000
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20 2 2.84000000 4.91902429 3.30000000
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21 1 2.13000000 6.14878037 0.00000000
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22 1 3.55000000 6.14878037 0.00000000
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23 2 3.55000000 6.14878037 3.30000000
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24 2 4.97000000 6.14878037 3.30000000
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25 1 0.00000000 7.37853644 0.00000000
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26 1 1.42000000 7.37853644 0.00000000
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27 2 1.42000000 7.37853644 3.30000000
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28 2 2.84000000 7.37853644 3.30000000
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29 1 2.13000000 8.60829251 0.00000000
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30 1 3.55000000 8.60829251 0.00000000
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31 2 3.55000000 8.60829251 3.30000000
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32 2 4.97000000 8.60829251 3.30000000
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33 1 0.00000000 9.83804859 0.00000000
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34 1 1.42000000 9.83804859 0.00000000
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35 2 1.42000000 9.83804859 3.30000000
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36 2 2.84000000 9.83804859 3.30000000
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37 1 2.13000000 11.06780466 0.00000000
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38 1 3.55000000 11.06780466 0.00000000
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39 2 3.55000000 11.06780466 3.30000000
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40 2 4.97000000 11.06780466 3.30000000
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41 1 0.00000000 12.29756073 0.00000000
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42 1 1.42000000 12.29756073 0.00000000
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43 2 1.42000000 12.29756073 3.30000000
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44 2 2.84000000 12.29756073 3.30000000
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45 1 2.13000000 13.52731681 0.00000000
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46 1 3.55000000 13.52731681 0.00000000
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47 2 3.55000000 13.52731681 3.30000000
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48 2 4.97000000 13.52731681 3.30000000
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49 1 0.00000000 14.75707288 0.00000000
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50 1 1.42000000 14.75707288 0.00000000
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51 2 1.42000000 14.75707288 3.30000000
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52 2 2.84000000 14.75707288 3.30000000
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53 1 2.13000000 15.98682895 0.00000000
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54 1 3.55000000 15.98682895 0.00000000
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55 2 3.55000000 15.98682895 3.30000000
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56 2 4.97000000 15.98682895 3.30000000
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57 1 0.00000000 17.21658503 0.00000000
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58 1 1.42000000 17.21658503 0.00000000
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59 2 1.42000000 17.21658503 3.30000000
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60 2 2.84000000 17.21658503 3.30000000
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61 1 2.13000000 18.44634110 0.00000000
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62 1 3.55000000 18.44634110 0.00000000
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63 2 3.55000000 18.44634110 3.30000000
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64 2 4.97000000 18.44634110 3.30000000
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65 1 4.26000000 0.00000000 0.00000000
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66 1 5.68000000 0.00000000 0.00000000
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67 2 5.68000000 0.00000000 3.30000000
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68 2 7.10000000 0.00000000 3.30000000
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69 1 6.39000000 1.22975607 0.00000000
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70 1 7.81000000 1.22975607 0.00000000
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71 2 7.81000000 1.22975607 3.30000000
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72 2 9.23000000 1.22975607 3.30000000
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73 1 4.26000000 2.45951215 0.00000000
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74 1 5.68000000 2.45951215 0.00000000
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75 2 5.68000000 2.45951215 3.30000000
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76 2 7.10000000 2.45951215 3.30000000
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77 1 6.39000000 3.68926822 0.00000000
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78 1 7.81000000 3.68926822 0.00000000
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79 2 7.81000000 3.68926822 3.30000000
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80 2 9.23000000 3.68926822 3.30000000
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81 1 4.26000000 4.91902429 0.00000000
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82 1 5.68000000 4.91902429 0.00000000
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83 2 5.68000000 4.91902429 3.30000000
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84 2 7.10000000 4.91902429 3.30000000
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85 1 6.39000000 6.14878037 0.00000000
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86 1 7.81000000 6.14878037 0.00000000
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87 2 7.81000000 6.14878037 3.30000000
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88 2 9.23000000 6.14878037 3.30000000
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89 1 4.26000000 7.37853644 0.00000000
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90 1 5.68000000 7.37853644 0.00000000
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91 2 5.68000000 7.37853644 3.30000000
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92 2 7.10000000 7.37853644 3.30000000
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93 1 6.39000000 8.60829251 0.00000000
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94 1 7.81000000 8.60829251 0.00000000
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95 2 7.81000000 8.60829251 3.30000000
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96 2 9.23000000 8.60829251 3.30000000
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97 1 4.26000000 9.83804859 0.00000000
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98 1 5.68000000 9.83804859 0.00000000
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99 2 5.68000000 9.83804859 3.30000000
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100 2 7.10000000 9.83804859 3.30000000
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101 1 6.39000000 11.06780466 0.00000000
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102 1 7.81000000 11.06780466 0.00000000
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103 2 7.81000000 11.06780466 3.30000000
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104 2 9.23000000 11.06780466 3.30000000
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105 1 4.26000000 12.29756073 0.00000000
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106 1 5.68000000 12.29756073 0.00000000
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107 2 5.68000000 12.29756073 3.30000000
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108 2 7.10000000 12.29756073 3.30000000
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109 1 6.39000000 13.52731681 0.00000000
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110 1 7.81000000 13.52731681 0.00000000
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111 2 7.81000000 13.52731681 3.30000000
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112 2 9.23000000 13.52731681 3.30000000
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113 1 4.26000000 14.75707288 0.00000000
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114 1 5.68000000 14.75707288 0.00000000
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115 2 5.68000000 14.75707288 3.30000000
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116 2 7.10000000 14.75707288 3.30000000
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117 1 6.39000000 15.98682895 0.00000000
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118 1 7.81000000 15.98682895 0.00000000
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119 2 7.81000000 15.98682895 3.30000000
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120 2 9.23000000 15.98682895 3.30000000
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121 1 4.26000000 17.21658503 0.00000000
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122 1 5.68000000 17.21658503 0.00000000
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123 2 5.68000000 17.21658503 3.30000000
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124 2 7.10000000 17.21658503 3.30000000
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125 1 6.39000000 18.44634110 0.00000000
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126 1 7.81000000 18.44634110 0.00000000
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127 2 7.81000000 18.44634110 3.30000000
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128 2 9.23000000 18.44634110 3.30000000
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129 1 8.52000000 0.00000000 0.00000000
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130 1 9.94000000 0.00000000 0.00000000
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131 2 9.94000000 0.00000000 3.30000000
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132 2 11.36000000 0.00000000 3.30000000
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133 1 10.65000000 1.22975607 0.00000000
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134 1 12.07000000 1.22975607 0.00000000
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135 2 12.07000000 1.22975607 3.30000000
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136 2 13.49000000 1.22975607 3.30000000
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137 1 8.52000000 2.45951215 0.00000000
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138 1 9.94000000 2.45951215 0.00000000
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139 2 9.94000000 2.45951215 3.30000000
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140 2 11.36000000 2.45951215 3.30000000
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141 1 10.65000000 3.68926822 0.00000000
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142 1 12.07000000 3.68926822 0.00000000
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143 2 12.07000000 3.68926822 3.30000000
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144 2 13.49000000 3.68926822 3.30000000
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145 1 8.52000000 4.91902429 0.00000000
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146 1 9.94000000 4.91902429 0.00000000
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147 2 9.94000000 4.91902429 3.30000000
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148 2 11.36000000 4.91902429 3.30000000
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149 1 10.65000000 6.14878037 0.00000000
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150 1 12.07000000 6.14878037 0.00000000
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151 2 12.07000000 6.14878037 3.30000000
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152 2 13.49000000 6.14878037 3.30000000
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153 1 8.52000000 7.37853644 0.00000000
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154 1 9.94000000 7.37853644 0.00000000
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155 2 9.94000000 7.37853644 3.30000000
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156 2 11.36000000 7.37853644 3.30000000
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157 1 10.65000000 8.60829251 0.00000000
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158 1 12.07000000 8.60829251 0.00000000
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159 2 12.07000000 8.60829251 3.30000000
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160 2 13.49000000 8.60829251 3.30000000
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161 1 8.52000000 9.83804859 0.00000000
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162 1 9.94000000 9.83804859 0.00000000
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163 2 9.94000000 9.83804859 3.30000000
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164 2 11.36000000 9.83804859 3.30000000
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165 1 10.65000000 11.06780466 0.00000000
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166 1 12.07000000 11.06780466 0.00000000
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167 2 12.07000000 11.06780466 3.30000000
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168 2 13.49000000 11.06780466 3.30000000
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169 1 8.52000000 12.29756073 0.00000000
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170 1 9.94000000 12.29756073 0.00000000
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171 2 9.94000000 12.29756073 3.30000000
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172 2 11.36000000 12.29756073 3.30000000
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173 1 10.65000000 13.52731681 0.00000000
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174 1 12.07000000 13.52731681 0.00000000
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175 2 12.07000000 13.52731681 3.30000000
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176 2 13.49000000 13.52731681 3.30000000
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177 1 8.52000000 14.75707288 0.00000000
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178 1 9.94000000 14.75707288 0.00000000
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179 2 9.94000000 14.75707288 3.30000000
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180 2 11.36000000 14.75707288 3.30000000
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181 1 10.65000000 15.98682895 0.00000000
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182 1 12.07000000 15.98682895 0.00000000
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183 2 12.07000000 15.98682895 3.30000000
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184 2 13.49000000 15.98682895 3.30000000
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185 1 8.52000000 17.21658503 0.00000000
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186 1 9.94000000 17.21658503 0.00000000
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187 2 9.94000000 17.21658503 3.30000000
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188 2 11.36000000 17.21658503 3.30000000
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189 1 10.65000000 18.44634110 0.00000000
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190 1 12.07000000 18.44634110 0.00000000
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191 2 12.07000000 18.44634110 3.30000000
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192 2 13.49000000 18.44634110 3.30000000
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193 1 12.78000000 0.00000000 0.00000000
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194 1 14.20000000 0.00000000 0.00000000
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195 2 14.20000000 0.00000000 3.30000000
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196 2 15.62000000 0.00000000 3.30000000
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197 1 14.91000000 1.22975607 0.00000000
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198 1 16.33000000 1.22975607 0.00000000
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199 2 16.33000000 1.22975607 3.30000000
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200 2 17.75000000 1.22975607 3.30000000
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201 1 12.78000000 2.45951215 0.00000000
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202 1 14.20000000 2.45951215 0.00000000
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203 2 14.20000000 2.45951215 3.30000000
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204 2 15.62000000 2.45951215 3.30000000
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205 1 14.91000000 3.68926822 0.00000000
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206 1 16.33000000 3.68926822 0.00000000
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207 2 16.33000000 3.68926822 3.30000000
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208 2 17.75000000 3.68926822 3.30000000
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209 1 12.78000000 4.91902429 0.00000000
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210 1 14.20000000 4.91902429 0.00000000
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211 2 14.20000000 4.91902429 3.30000000
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212 2 15.62000000 4.91902429 3.30000000
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213 1 14.91000000 6.14878037 0.00000000
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214 1 16.33000000 6.14878037 0.00000000
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215 2 16.33000000 6.14878037 3.30000000
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216 2 17.75000000 6.14878037 3.30000000
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217 1 12.78000000 7.37853644 0.00000000
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218 1 14.20000000 7.37853644 0.00000000
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219 2 14.20000000 7.37853644 3.30000000
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220 2 15.62000000 7.37853644 3.30000000
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221 1 14.91000000 8.60829251 0.00000000
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222 1 16.33000000 8.60829251 0.00000000
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223 2 16.33000000 8.60829251 3.30000000
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224 2 17.75000000 8.60829251 3.30000000
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225 1 12.78000000 9.83804859 0.00000000
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226 1 14.20000000 9.83804859 0.00000000
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227 2 14.20000000 9.83804859 3.30000000
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228 2 15.62000000 9.83804859 3.30000000
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229 1 14.91000000 11.06780466 0.00000000
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230 1 16.33000000 11.06780466 0.00000000
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231 2 16.33000000 11.06780466 3.30000000
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232 2 17.75000000 11.06780466 3.30000000
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233 1 12.78000000 12.29756073 0.00000000
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234 1 14.20000000 12.29756073 0.00000000
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235 2 14.20000000 12.29756073 3.30000000
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236 2 15.62000000 12.29756073 3.30000000
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237 1 14.91000000 13.52731681 0.00000000
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238 1 16.33000000 13.52731681 0.00000000
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239 2 16.33000000 13.52731681 3.30000000
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240 2 17.75000000 13.52731681 3.30000000
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241 1 12.78000000 14.75707288 0.00000000
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242 1 14.20000000 14.75707288 0.00000000
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243 2 14.20000000 14.75707288 3.30000000
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244 2 15.62000000 14.75707288 3.30000000
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245 1 14.91000000 15.98682895 0.00000000
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246 1 16.33000000 15.98682895 0.00000000
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247 2 16.33000000 15.98682895 3.30000000
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248 2 17.75000000 15.98682895 3.30000000
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249 1 12.78000000 17.21658503 0.00000000
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250 1 14.20000000 17.21658503 0.00000000
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251 2 14.20000000 17.21658503 3.30000000
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252 2 15.62000000 17.21658503 3.30000000
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253 1 14.91000000 18.44634110 0.00000000
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254 1 16.33000000 18.44634110 0.00000000
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255 2 16.33000000 18.44634110 3.30000000
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256 2 17.75000000 18.44634110 3.30000000
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@ -1,139 +0,0 @@
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info: xyz2data 11:52, Tue 28-02-2017
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129 atoms
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2 atom types
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0.00000000 17.04000000 xlo xhi
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0.00000000 19.67609717 ylo yhi
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-10.00000000 40.00000000 zlo zhi
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Atoms
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1 1 0.00000000 0.00000000 0.00000000
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2 1 1.42000000 0.00000000 0.00000000
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3 1 2.13000000 1.22975607 0.00000000
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4 1 3.55000000 1.22975607 0.00000000
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5 1 0.00000000 2.45951215 0.00000000
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6 1 1.42000000 2.45951215 0.00000000
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7 1 2.13000000 3.68926822 0.00000000
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8 1 3.55000000 3.68926822 0.00000000
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9 1 0.00000000 4.91902429 0.00000000
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10 1 1.42000000 4.91902429 0.00000000
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11 1 2.13000000 6.14878037 0.00000000
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12 1 3.55000000 6.14878037 0.00000000
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13 1 0.00000000 7.37853644 0.00000000
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14 1 1.42000000 7.37853644 0.00000000
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15 1 2.13000000 8.60829251 0.00000000
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16 1 3.55000000 8.60829251 0.00000000
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17 1 0.00000000 9.83804859 0.00000000
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18 1 1.42000000 9.83804859 0.00000000
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19 1 2.13000000 11.06780466 0.00000000
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20 1 3.55000000 11.06780466 0.00000000
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21 1 0.00000000 12.29756073 0.00000000
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22 1 1.42000000 12.29756073 0.00000000
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23 1 2.13000000 13.52731681 0.00000000
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24 1 3.55000000 13.52731681 0.00000000
|
|
||||||
25 1 0.00000000 14.75707288 0.00000000
|
|
||||||
26 1 1.42000000 14.75707288 0.00000000
|
|
||||||
27 1 2.13000000 15.98682895 0.00000000
|
|
||||||
28 1 3.55000000 15.98682895 0.00000000
|
|
||||||
29 1 0.00000000 17.21658503 0.00000000
|
|
||||||
30 1 1.42000000 17.21658503 0.00000000
|
|
||||||
31 1 2.13000000 18.44634110 0.00000000
|
|
||||||
32 1 3.55000000 18.44634110 0.00000000
|
|
||||||
33 1 4.26000000 0.00000000 0.00000000
|
|
||||||
34 1 5.68000000 0.00000000 0.00000000
|
|
||||||
35 1 6.39000000 1.22975607 0.00000000
|
|
||||||
36 1 7.81000000 1.22975607 0.00000000
|
|
||||||
37 1 4.26000000 2.45951215 0.00000000
|
|
||||||
38 1 5.68000000 2.45951215 0.00000000
|
|
||||||
39 1 6.39000000 3.68926822 0.00000000
|
|
||||||
40 1 7.81000000 3.68926822 0.00000000
|
|
||||||
41 1 4.26000000 4.91902429 0.00000000
|
|
||||||
42 1 5.68000000 4.91902429 0.00000000
|
|
||||||
43 1 6.39000000 6.14878037 0.00000000
|
|
||||||
44 1 7.81000000 6.14878037 0.00000000
|
|
||||||
45 1 4.26000000 7.37853644 0.00000000
|
|
||||||
46 1 5.68000000 7.37853644 0.00000000
|
|
||||||
47 1 6.39000000 8.60829251 0.00000000
|
|
||||||
48 1 7.81000000 8.60829251 0.00000000
|
|
||||||
49 1 4.26000000 9.83804859 0.00000000
|
|
||||||
50 1 5.68000000 9.83804859 0.00000000
|
|
||||||
51 1 6.39000000 11.06780466 0.00000000
|
|
||||||
52 1 7.81000000 11.06780466 0.00000000
|
|
||||||
53 1 4.26000000 12.29756073 0.00000000
|
|
||||||
54 1 5.68000000 12.29756073 0.00000000
|
|
||||||
55 1 6.39000000 13.52731681 0.00000000
|
|
||||||
56 1 7.81000000 13.52731681 0.00000000
|
|
||||||
57 1 4.26000000 14.75707288 0.00000000
|
|
||||||
58 1 5.68000000 14.75707288 0.00000000
|
|
||||||
59 1 6.39000000 15.98682895 0.00000000
|
|
||||||
60 1 7.81000000 15.98682895 0.00000000
|
|
||||||
61 1 4.26000000 17.21658503 0.00000000
|
|
||||||
62 1 5.68000000 17.21658503 0.00000000
|
|
||||||
63 1 6.39000000 18.44634110 0.00000000
|
|
||||||
64 1 7.81000000 18.44634110 0.00000000
|
|
||||||
65 1 8.52000000 0.00000000 0.00000000
|
|
||||||
66 1 9.94000000 0.00000000 0.00000000
|
|
||||||
67 1 10.65000000 1.22975607 0.00000000
|
|
||||||
68 1 12.07000000 1.22975607 0.00000000
|
|
||||||
69 1 8.52000000 2.45951215 0.00000000
|
|
||||||
70 1 9.94000000 2.45951215 0.00000000
|
|
||||||
71 1 10.65000000 3.68926822 0.00000000
|
|
||||||
72 1 12.07000000 3.68926822 0.00000000
|
|
||||||
73 1 8.52000000 4.91902429 0.00000000
|
|
||||||
74 1 9.94000000 4.91902429 0.00000000
|
|
||||||
75 1 10.65000000 6.14878037 0.00000000
|
|
||||||
76 1 12.07000000 6.14878037 0.00000000
|
|
||||||
77 1 8.52000000 7.37853644 0.00000000
|
|
||||||
78 1 9.94000000 7.37853644 0.00000000
|
|
||||||
79 1 10.65000000 8.60829251 0.00000000
|
|
||||||
80 1 12.07000000 8.60829251 0.00000000
|
|
||||||
81 1 8.52000000 9.83804859 0.00000000
|
|
||||||
82 1 9.94000000 9.83804859 0.00000000
|
|
||||||
83 1 10.65000000 11.06780466 0.00000000
|
|
||||||
84 1 12.07000000 11.06780466 0.00000000
|
|
||||||
85 1 8.52000000 12.29756073 0.00000000
|
|
||||||
86 1 9.94000000 12.29756073 0.00000000
|
|
||||||
87 1 10.65000000 13.52731681 0.00000000
|
|
||||||
88 1 12.07000000 13.52731681 0.00000000
|
|
||||||
89 1 8.52000000 14.75707288 0.00000000
|
|
||||||
90 1 9.94000000 14.75707288 0.00000000
|
|
||||||
91 1 10.65000000 15.98682895 0.00000000
|
|
||||||
92 1 12.07000000 15.98682895 0.00000000
|
|
||||||
93 1 8.52000000 17.21658503 0.00000000
|
|
||||||
94 1 9.94000000 17.21658503 0.00000000
|
|
||||||
95 1 10.65000000 18.44634110 0.00000000
|
|
||||||
96 1 12.07000000 18.44634110 0.00000000
|
|
||||||
97 1 12.78000000 0.00000000 0.00000000
|
|
||||||
98 1 14.20000000 0.00000000 0.00000000
|
|
||||||
99 1 14.91000000 1.22975607 0.00000000
|
|
||||||
100 1 16.33000000 1.22975607 0.00000000
|
|
||||||
101 1 12.78000000 2.45951215 0.00000000
|
|
||||||
102 1 14.20000000 2.45951215 0.00000000
|
|
||||||
103 1 14.91000000 3.68926822 0.00000000
|
|
||||||
104 1 16.33000000 3.68926822 0.00000000
|
|
||||||
105 1 12.78000000 4.91902429 0.00000000
|
|
||||||
106 1 14.20000000 4.91902429 0.00000000
|
|
||||||
107 1 14.91000000 6.14878037 0.00000000
|
|
||||||
108 1 16.33000000 6.14878037 0.00000000
|
|
||||||
109 1 12.78000000 7.37853644 0.00000000
|
|
||||||
110 1 14.20000000 7.37853644 0.00000000
|
|
||||||
111 1 14.91000000 8.60829251 0.00000000
|
|
||||||
112 1 16.33000000 8.60829251 0.00000000
|
|
||||||
113 1 12.78000000 9.83804859 0.00000000
|
|
||||||
114 1 14.20000000 9.83804859 0.00000000
|
|
||||||
115 1 14.91000000 11.06780466 0.00000000
|
|
||||||
116 1 16.33000000 11.06780466 0.00000000
|
|
||||||
117 1 12.78000000 12.29756073 0.00000000
|
|
||||||
118 1 14.20000000 12.29756073 0.00000000
|
|
||||||
119 1 14.91000000 13.52731681 0.00000000
|
|
||||||
120 1 16.33000000 13.52731681 0.00000000
|
|
||||||
121 1 12.78000000 14.75707288 0.00000000
|
|
||||||
122 1 14.20000000 14.75707288 0.00000000
|
|
||||||
123 1 14.91000000 15.98682895 0.00000000
|
|
||||||
124 1 16.33000000 15.98682895 0.00000000
|
|
||||||
125 1 12.78000000 17.21658503 0.00000000
|
|
||||||
126 1 14.20000000 17.21658503 0.00000000
|
|
||||||
127 1 14.91000000 18.44634110 0.00000000
|
|
||||||
128 1 16.33000000 18.44634110 0.00000000
|
|
||||||
129 2 10.00000000 10.00000000 3.30000000
|
|
||||||
@ -1,45 +0,0 @@
|
|||||||
# Initialization
|
|
||||||
units metal
|
|
||||||
boundary p p p
|
|
||||||
atom_style atomic
|
|
||||||
processors * * 1 # domain decomposition over x and y
|
|
||||||
|
|
||||||
# System and atom definition
|
|
||||||
# we use 2 atom types so that inter- and intra-layer
|
|
||||||
# interactions can be specified separately
|
|
||||||
read_data data.graphene-adsorbant # read lammps data file
|
|
||||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
|
||||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
|
||||||
# Neighbor update settings
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify every 1
|
|
||||||
neigh_modify delay 0
|
|
||||||
neigh_modify check yes
|
|
||||||
# Separate atom groups
|
|
||||||
group membrane type 1
|
|
||||||
group adsorbant type 2
|
|
||||||
|
|
||||||
######################## Potential defition ########################
|
|
||||||
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
|
|
||||||
####################################################################
|
|
||||||
pair_coeff * * none
|
|
||||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
|
||||||
####################################################################
|
|
||||||
|
|
||||||
#### Simulation settings ####
|
|
||||||
timestep 0.0001
|
|
||||||
fix thermostat adsorbant nve
|
|
||||||
fix rigid_membrane membrane setforce 0 0 0
|
|
||||||
compute COM1 membrane com
|
|
||||||
compute COM2 adsorbant com
|
|
||||||
############################
|
|
||||||
|
|
||||||
# Output
|
|
||||||
#dump 1 all xyz 100 trajec.xyz
|
|
||||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
|
||||||
thermo 100
|
|
||||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
|
||||||
thermo_modify line one format float %14.8f
|
|
||||||
|
|
||||||
###### Run molecular dynamics ######
|
|
||||||
run 10000
|
|
||||||
@ -1,45 +0,0 @@
|
|||||||
# Initialization
|
|
||||||
units metal
|
|
||||||
boundary p p p
|
|
||||||
atom_style atomic
|
|
||||||
processors * * 1 # domain decomposition over x and y
|
|
||||||
|
|
||||||
# System and atom definition
|
|
||||||
# we use 2 atom types so that inter- and intra-layer
|
|
||||||
# interactions can be specified separately
|
|
||||||
read_data data.bilayer-graphene # read lammps data file
|
|
||||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
|
||||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
|
||||||
# Neighbor update settings
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify every 1
|
|
||||||
neigh_modify delay 0
|
|
||||||
neigh_modify check yes
|
|
||||||
# Separate atom groups
|
|
||||||
group membrane type 1
|
|
||||||
group adsorbant type 2
|
|
||||||
|
|
||||||
######################## Potential defition ########################
|
|
||||||
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
|
|
||||||
####################################################################
|
|
||||||
pair_coeff * * rebo CH.airebo C C # chemical
|
|
||||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
|
||||||
####################################################################
|
|
||||||
|
|
||||||
#### Simulation settings ####
|
|
||||||
timestep 0.0001
|
|
||||||
velocity all create 300.0 12345
|
|
||||||
fix thermostat all nve
|
|
||||||
compute COM1 membrane com
|
|
||||||
compute COM2 adsorbant com
|
|
||||||
############################
|
|
||||||
|
|
||||||
# Output
|
|
||||||
#dump 1 all xyz 100 trajec.xyz
|
|
||||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
|
||||||
thermo 10
|
|
||||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
|
||||||
thermo_modify line one format float %14.8f
|
|
||||||
|
|
||||||
###### Run molecular dynamics ######
|
|
||||||
run 1000
|
|
||||||
@ -49,12 +49,12 @@ variable KC equal c_1
|
|||||||
|
|
||||||
# Output
|
# Output
|
||||||
thermo 100
|
thermo 100
|
||||||
thermo_style custom step cpu etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||||
thermo_modify line one format float %.16f
|
thermo_modify line one format float %.10f
|
||||||
thermo_modify flush yes norm no lost warn #ignore
|
thermo_modify flush yes norm no lost warn #ignore
|
||||||
|
|
||||||
dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||||
dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||||
|
|
||||||
###### Run molecular dynamics ######
|
###### Run molecular dynamics ######
|
||||||
run 10000
|
run 1000
|
||||||
|
|||||||
1
examples/USER/misc/kolmogorov_crespi_z/CC.KC
Symbolic link
1
examples/USER/misc/kolmogorov_crespi_z/CC.KC
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../../potentials/CC.KC
|
||||||
1
examples/USER/misc/kolmogorov_crespi_z/CH.airebo
Symbolic link
1
examples/USER/misc/kolmogorov_crespi_z/CH.airebo
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../../potentials/CH.airebo
|
||||||
@ -1,4 +1,5 @@
|
|||||||
LAMMPS (17 Nov 2016)
|
LAMMPS (8 Mar 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Initialization
|
# Initialization
|
||||||
units metal
|
units metal
|
||||||
boundary p p p
|
boundary p p p
|
||||||
@ -51,13 +52,23 @@ thermo_modify line one format float %14.8f
|
|||||||
###### Run molecular dynamics ######
|
###### Run molecular dynamics ######
|
||||||
run 10000
|
run 10000
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
2 neighbor list requests
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 16
|
master list distance cutoff = 16
|
||||||
ghost atom cutoff = 16
|
ghost atom cutoff = 16
|
||||||
binsize = 8 -> bins = 3 3 7
|
binsize = 8, bins = 3 3 7
|
||||||
Memory usage per processor = 2.48399 Mbytes
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair kolmogorov/crespi/z, perpetual, skip from (2)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) neighbor class addition, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.206 | 3.206 | 3.206 Mbytes
|
||||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||||
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
|
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
|
||||||
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
|
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
|
||||||
@ -160,20 +171,20 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
|||||||
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
|
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
|
||||||
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
|
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
|
||||||
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
|
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
|
||||||
Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
|
Loop time of 0.34689 on 1 procs for 10000 steps with 129 atoms
|
||||||
|
|
||||||
Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
|
Performance: 249.070 ns/day, 0.096 hours/ns, 28827.585 timesteps/s
|
||||||
131.8% CPU use with 1 MPI tasks x no OpenMP threads
|
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
|
Pair | 0.2028 | 0.2028 | 0.2028 | 0.0 | 58.46
|
||||||
Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
|
Neigh | 0.00021529 | 0.00021529 | 0.00021529 | 0.0 | 0.06
|
||||||
Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
|
Comm | 0.10656 | 0.10656 | 0.10656 | 0.0 | 30.72
|
||||||
Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
|
Output | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.44
|
||||||
Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
|
Modify | 0.011605 | 0.011605 | 0.011605 | 0.0 | 3.35
|
||||||
Other | | 0.01361 | | | 3.56
|
Other | | 0.0242 | | | 6.98
|
||||||
|
|
||||||
Nlocal: 129 ave 129 max 129 min
|
Nlocal: 129 ave 129 max 129 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
@ -1,4 +1,5 @@
|
|||||||
LAMMPS (17 Nov 2016)
|
LAMMPS (8 Mar 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Initialization
|
# Initialization
|
||||||
units metal
|
units metal
|
||||||
boundary p p p
|
boundary p p p
|
||||||
@ -10,7 +11,7 @@ processors * * 1 # domain decomposition over x and y
|
|||||||
# interactions can be specified separately
|
# interactions can be specified separately
|
||||||
read_data data.graphene-adsorbant # read lammps data file
|
read_data data.graphene-adsorbant # read lammps data file
|
||||||
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
|
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
|
||||||
1 by 1 by 1 MPI processor grid
|
2 by 2 by 1 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
129 atoms
|
129 atoms
|
||||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||||
@ -51,13 +52,23 @@ thermo_modify line one format float %14.8f
|
|||||||
###### Run molecular dynamics ######
|
###### Run molecular dynamics ######
|
||||||
run 10000
|
run 10000
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
2 neighbor list requests
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 16
|
master list distance cutoff = 16
|
||||||
ghost atom cutoff = 16
|
ghost atom cutoff = 16
|
||||||
binsize = 8 -> bins = 3 3 7
|
binsize = 8, bins = 3 3 7
|
||||||
Memory usage per processor = 2.48399 Mbytes
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair kolmogorov/crespi/z, perpetual, skip from (2)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) neighbor class addition, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.167 | 3.167 | 3.168 Mbytes
|
||||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||||
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
|
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
|
||||||
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
|
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
|
||||||
@ -160,27 +171,27 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
|||||||
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
|
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
|
||||||
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
|
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
|
||||||
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
|
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
|
||||||
Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
|
Loop time of 0.524797 on 4 procs for 10000 steps with 129 atoms
|
||||||
|
|
||||||
Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
|
Performance: 164.635 ns/day, 0.146 hours/ns, 19054.971 timesteps/s
|
||||||
131.8% CPU use with 1 MPI tasks x no OpenMP threads
|
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
|
Pair | 0.043099 | 0.060851 | 0.10153 | 9.7 | 11.60
|
||||||
Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
|
Neigh | 6.2704e-05 | 6.628e-05 | 6.8188e-05 | 0.0 | 0.01
|
||||||
Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
|
Comm | 0.35059 | 0.39384 | 0.41232 | 4.0 | 75.05
|
||||||
Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
|
Output | 0.0028515 | 0.0031345 | 0.0037408 | 0.6 | 0.60
|
||||||
Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
|
Modify | 0.0063083 | 0.0065277 | 0.0066838 | 0.2 | 1.24
|
||||||
Other | | 0.01361 | | | 3.56
|
Other | | 0.06038 | | | 11.50
|
||||||
|
|
||||||
Nlocal: 129 ave 129 max 129 min
|
Nlocal: 32.25 ave 33 max 32 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
Nghost: 1867 ave 1867 max 1867 min
|
Nghost: 1305.75 ave 1306 max 1305 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
Neighs: 290 ave 290 max 290 min
|
Neighs: 72.5 ave 144 max 43 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
Total # of neighbors = 290
|
Total # of neighbors = 290
|
||||||
Ave neighs/atom = 2.24806
|
Ave neighs/atom = 2.24806
|
||||||
@ -1,4 +1,5 @@
|
|||||||
LAMMPS (17 Nov 2016)
|
LAMMPS (8 Mar 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Initialization
|
# Initialization
|
||||||
units metal
|
units metal
|
||||||
boundary p p p
|
boundary p p p
|
||||||
@ -10,7 +11,7 @@ processors * * 1 # domain decomposition over x and y
|
|||||||
# interactions can be specified separately
|
# interactions can be specified separately
|
||||||
read_data data.bilayer-graphene # read lammps data file
|
read_data data.bilayer-graphene # read lammps data file
|
||||||
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
|
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
|
||||||
2 by 2 by 1 MPI processor grid
|
1 by 1 by 1 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
256 atoms
|
256 atoms
|
||||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||||
@ -52,13 +53,28 @@ thermo_modify line one format float %14.8f
|
|||||||
###### Run molecular dynamics ######
|
###### Run molecular dynamics ######
|
||||||
run 1000
|
run 1000
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
3 neighbor list requests
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 16
|
master list distance cutoff = 16
|
||||||
ghost atom cutoff = 16
|
ghost atom cutoff = 16
|
||||||
binsize = 8 -> bins = 3 3 8
|
binsize = 8, bins = 3 3 8
|
||||||
Memory usage per processor = 3.22197 Mbytes
|
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||||
|
(1) pair rebo, perpetual
|
||||||
|
attributes: full, newton on, ghost
|
||||||
|
pair build: full/bin/ghost
|
||||||
|
stencil: full/ghost/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) neighbor class addition, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
|
||||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||||
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
|
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
|
||||||
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
|
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
|
||||||
@ -161,32 +177,32 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
|||||||
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
|
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
|
||||||
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
|
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
|
||||||
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
|
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
|
||||||
Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
|
Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms
|
||||||
|
|
||||||
Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
|
Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 timesteps/s
|
||||||
120.2% CPU use with 4 MPI tasks x no OpenMP threads
|
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
|
Pair | 3.8786 | 3.8786 | 3.8786 | 0.0 | 99.41
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
|
Comm | 0.010816 | 0.010816 | 0.010816 | 0.0 | 0.28
|
||||||
Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
|
Output | 0.002461 | 0.002461 | 0.002461 | 0.0 | 0.06
|
||||||
Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
|
Modify | 0.0051703 | 0.0051703 | 0.0051703 | 0.0 | 0.13
|
||||||
Other | | 0.008904 | | | 0.40
|
Other | | 0.004447 | | | 0.11
|
||||||
|
|
||||||
Nlocal: 64 ave 64 max 64 min
|
Nlocal: 256 ave 256 max 256 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 1265 ave 1265 max 1265 min
|
Nghost: 1721 ave 1721 max 1721 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 11824 ave 11824 max 11824 min
|
Neighs: 37312 ave 37312 max 37312 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
FullNghs: 23648 ave 23648 max 23648 min
|
FullNghs: 94592 ave 94592 max 94592 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 94592
|
Total # of neighbors = 94592
|
||||||
Ave neighs/atom = 369.5
|
Ave neighs/atom = 369.5
|
||||||
Neighbor list builds = 0
|
Neighbor list builds = 0
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
Total wall time: 0:00:02
|
Total wall time: 0:00:03
|
||||||
@ -1,4 +1,5 @@
|
|||||||
LAMMPS (17 Nov 2016)
|
LAMMPS (8 Mar 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Initialization
|
# Initialization
|
||||||
units metal
|
units metal
|
||||||
boundary p p p
|
boundary p p p
|
||||||
@ -52,13 +53,28 @@ thermo_modify line one format float %14.8f
|
|||||||
###### Run molecular dynamics ######
|
###### Run molecular dynamics ######
|
||||||
run 1000
|
run 1000
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
3 neighbor list requests
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 16
|
master list distance cutoff = 16
|
||||||
ghost atom cutoff = 16
|
ghost atom cutoff = 16
|
||||||
binsize = 8 -> bins = 3 3 8
|
binsize = 8, bins = 3 3 8
|
||||||
Memory usage per processor = 3.22197 Mbytes
|
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||||
|
(1) pair rebo, perpetual
|
||||||
|
attributes: full, newton on, ghost
|
||||||
|
pair build: full/bin/ghost
|
||||||
|
stencil: full/ghost/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) neighbor class addition, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
|
||||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||||
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
|
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
|
||||||
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
|
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
|
||||||
@ -161,26 +177,26 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
|||||||
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
|
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
|
||||||
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
|
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
|
||||||
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
|
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
|
||||||
Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
|
Loop time of 1.32192 on 4 procs for 1000 steps with 256 atoms
|
||||||
|
|
||||||
Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
|
Performance: 6.536 ns/day, 3.672 hours/ns, 756.476 timesteps/s
|
||||||
120.2% CPU use with 4 MPI tasks x no OpenMP threads
|
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
|
Pair | 1.1157 | 1.172 | 1.2369 | 4.0 | 88.66
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
|
Comm | 0.071678 | 0.13667 | 0.19304 | 11.8 | 10.34
|
||||||
Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
|
Output | 0.0029244 | 0.0031272 | 0.0035112 | 0.4 | 0.24
|
||||||
Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
|
Modify | 0.0016961 | 0.0017477 | 0.0017846 | 0.1 | 0.13
|
||||||
Other | | 0.008904 | | | 0.40
|
Other | | 0.008334 | | | 0.63
|
||||||
|
|
||||||
Nlocal: 64 ave 64 max 64 min
|
Nlocal: 64 ave 64 max 64 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 1265 ave 1265 max 1265 min
|
Nghost: 1265 ave 1265 max 1265 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 11824 ave 11824 max 11824 min
|
Neighs: 9328 ave 9328 max 9328 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
FullNghs: 23648 ave 23648 max 23648 min
|
FullNghs: 23648 ave 23648 max 23648 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
@ -189,4 +205,4 @@ Total # of neighbors = 94592
|
|||||||
Ave neighs/atom = 369.5
|
Ave neighs/atom = 369.5
|
||||||
Neighbor list builds = 0
|
Neighbor list builds = 0
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
Total wall time: 0:00:02
|
Total wall time: 0:00:01
|
||||||
Reference in New Issue
Block a user