updated ScaFaCoS examples, added open-boundary Hammersley distributed sphere and charged cloud near a charged wall examples
This commit is contained in:
Rene Halver
@ -1,25 +1,25 @@
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LAMMPS Description
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8 atoms
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2 atom types
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0.0000000000000000 2.000000000000000 xlo xhi
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0.0000000000000000 2.000000000000000 ylo yhi
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0.0000000000000000 2.000000000000000 zlo zhi
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Masses
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1 22.98976928
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2 35.45
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Atoms
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1 1 1.0 0.0 0.0 0.0
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2 2 -1.0 1.0 0.0 0.0
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3 2 -1.0 0.0 1.0 0.0
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4 1 1.0 1.0 1.0 0.0
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5 2 -1.0 0.0 0.0 1.0
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6 1 1.0 1.0 0.0 1.0
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7 1 1.0 0.0 1.0 1.0
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8 2 -1.0 1.0 1.0 1.0
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LAMMPS Description
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|
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8 atoms
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2 atom types
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0 2 xlo xhi
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0 2 ylo yhi
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0 2 zlo zhi
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Masses
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||||
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1 22.98976928
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2 35.45
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Atoms
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1 2 1 0 0 0
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2 1 -1 1 0 0
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3 1 -1 0 1 0
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4 2 1 1 1 0
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5 1 -1 0 0 1
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6 2 1 1 0 1
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7 2 1 0 1 1
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8 1 -1 1 1 1
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316
examples/USER/scafacos/data.cloud_wall
Normal file
316
examples/USER/scafacos/data.cloud_wall
Normal file
@ -0,0 +1,316 @@
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LAMMPS Description
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300 atoms
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1 atom types
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0 10 xlo xhi
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0 10 ylo yhi
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0 10 zlo zhi
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Masses
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1 1.0
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Atoms
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1 1 1 0 0 4.5
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2 1 -1 0 0 5.5
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3 1 1 0 1 4.5
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4 1 -1 0 1 5.5
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5 1 1 0 2 4.5
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6 1 -1 0 2 5.5
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7 1 1 0 3 4.5
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8 1 -1 0 3 5.5
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9 1 1 0 4 4.5
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10 1 -1 0 4 5.5
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11 1 1 0 5 4.5
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12 1 -1 0 5 5.5
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13 1 1 0 6 4.5
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14 1 -1 0 6 5.5
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15 1 1 0 7 4.5
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16 1 -1 0 7 5.5
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17 1 1 0 8 4.5
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18 1 -1 0 8 5.5
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19 1 1 0 9 4.5
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20 1 -1 0 9 5.5
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21 1 1 1 0 4.5
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22 1 -1 1 0 5.5
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23 1 1 1 1 4.5
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24 1 -1 1 1 5.5
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25 1 1 1 2 4.5
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26 1 -1 1 2 5.5
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27 1 1 1 3 4.5
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28 1 -1 1 3 5.5
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29 1 1 1 4 4.5
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30 1 -1 1 4 5.5
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31 1 1 1 5 4.5
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32 1 -1 1 5 5.5
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33 1 1 1 6 4.5
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34 1 -1 1 6 5.5
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35 1 1 1 7 4.5
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36 1 -1 1 7 5.5
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37 1 1 1 8 4.5
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38 1 -1 1 8 5.5
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||||
39 1 1 1 9 4.5
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40 1 -1 1 9 5.5
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41 1 1 2 0 4.5
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42 1 -1 2 0 5.5
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43 1 1 2 1 4.5
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44 1 -1 2 1 5.5
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45 1 1 2 2 4.5
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46 1 -1 2 2 5.5
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47 1 1 2 3 4.5
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48 1 -1 2 3 5.5
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49 1 1 2 4 4.5
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50 1 -1 2 4 5.5
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51 1 1 2 5 4.5
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52 1 -1 2 5 5.5
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53 1 1 2 6 4.5
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54 1 -1 2 6 5.5
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55 1 1 2 7 4.5
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56 1 -1 2 7 5.5
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57 1 1 2 8 4.5
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58 1 -1 2 8 5.5
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59 1 1 2 9 4.5
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60 1 -1 2 9 5.5
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61 1 1 3 0 4.5
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62 1 -1 3 0 5.5
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63 1 1 3 1 4.5
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64 1 -1 3 1 5.5
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65 1 1 3 2 4.5
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66 1 -1 3 2 5.5
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67 1 1 3 3 4.5
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68 1 -1 3 3 5.5
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69 1 1 3 4 4.5
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70 1 -1 3 4 5.5
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71 1 1 3 5 4.5
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72 1 -1 3 5 5.5
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73 1 1 3 6 4.5
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74 1 -1 3 6 5.5
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75 1 1 3 7 4.5
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76 1 -1 3 7 5.5
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77 1 1 3 8 4.5
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78 1 -1 3 8 5.5
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79 1 1 3 9 4.5
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80 1 -1 3 9 5.5
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81 1 1 4 0 4.5
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82 1 -1 4 0 5.5
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83 1 1 4 1 4.5
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84 1 -1 4 1 5.5
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85 1 1 4 2 4.5
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86 1 -1 4 2 5.5
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87 1 1 4 3 4.5
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88 1 -1 4 3 5.5
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89 1 1 4 4 4.5
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90 1 -1 4 4 5.5
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91 1 1 4 5 4.5
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92 1 -1 4 5 5.5
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93 1 1 4 6 4.5
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94 1 -1 4 6 5.5
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95 1 1 4 7 4.5
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96 1 -1 4 7 5.5
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97 1 1 4 8 4.5
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98 1 -1 4 8 5.5
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99 1 1 4 9 4.5
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100 1 -1 4 9 5.5
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101 1 1 5 0 4.5
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102 1 -1 5 0 5.5
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103 1 1 5 1 4.5
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104 1 -1 5 1 5.5
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105 1 1 5 2 4.5
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106 1 -1 5 2 5.5
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107 1 1 5 3 4.5
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108 1 -1 5 3 5.5
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109 1 1 5 4 4.5
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110 1 -1 5 4 5.5
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111 1 1 5 5 4.5
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112 1 -1 5 5 5.5
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113 1 1 5 6 4.5
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114 1 -1 5 6 5.5
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115 1 1 5 7 4.5
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116 1 -1 5 7 5.5
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117 1 1 5 8 4.5
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118 1 -1 5 8 5.5
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119 1 1 5 9 4.5
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120 1 -1 5 9 5.5
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121 1 1 6 0 4.5
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122 1 -1 6 0 5.5
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123 1 1 6 1 4.5
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124 1 -1 6 1 5.5
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125 1 1 6 2 4.5
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126 1 -1 6 2 5.5
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127 1 1 6 3 4.5
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128 1 -1 6 3 5.5
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129 1 1 6 4 4.5
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130 1 -1 6 4 5.5
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131 1 1 6 5 4.5
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||||
132 1 -1 6 5 5.5
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||||
133 1 1 6 6 4.5
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134 1 -1 6 6 5.5
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135 1 1 6 7 4.5
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136 1 -1 6 7 5.5
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137 1 1 6 8 4.5
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138 1 -1 6 8 5.5
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||||
139 1 1 6 9 4.5
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140 1 -1 6 9 5.5
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141 1 1 7 0 4.5
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142 1 -1 7 0 5.5
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||||
143 1 1 7 1 4.5
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144 1 -1 7 1 5.5
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145 1 1 7 2 4.5
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146 1 -1 7 2 5.5
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147 1 1 7 3 4.5
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148 1 -1 7 3 5.5
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149 1 1 7 4 4.5
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150 1 -1 7 4 5.5
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151 1 1 7 5 4.5
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152 1 -1 7 5 5.5
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153 1 1 7 6 4.5
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154 1 -1 7 6 5.5
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155 1 1 7 7 4.5
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156 1 -1 7 7 5.5
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157 1 1 7 8 4.5
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158 1 -1 7 8 5.5
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159 1 1 7 9 4.5
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||||
160 1 -1 7 9 5.5
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161 1 1 8 0 4.5
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||||
162 1 -1 8 0 5.5
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||||
163 1 1 8 1 4.5
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164 1 -1 8 1 5.5
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165 1 1 8 2 4.5
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166 1 -1 8 2 5.5
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||||
167 1 1 8 3 4.5
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168 1 -1 8 3 5.5
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169 1 1 8 4 4.5
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170 1 -1 8 4 5.5
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171 1 1 8 5 4.5
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172 1 -1 8 5 5.5
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||||
173 1 1 8 6 4.5
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||||
174 1 -1 8 6 5.5
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||||
175 1 1 8 7 4.5
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||||
176 1 -1 8 7 5.5
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||||
177 1 1 8 8 4.5
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178 1 -1 8 8 5.5
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||||
179 1 1 8 9 4.5
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||||
180 1 -1 8 9 5.5
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181 1 1 9 0 4.5
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||||
182 1 -1 9 0 5.5
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||||
183 1 1 9 1 4.5
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184 1 -1 9 1 5.5
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185 1 1 9 2 4.5
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||||
186 1 -1 9 2 5.5
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187 1 1 9 3 4.5
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188 1 -1 9 3 5.5
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189 1 1 9 4 4.5
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190 1 -1 9 4 5.5
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191 1 1 9 5 4.5
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192 1 -1 9 5 5.5
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193 1 1 9 6 4.5
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194 1 -1 9 6 5.5
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195 1 1 9 7 4.5
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196 1 -1 9 7 5.5
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197 1 1 9 8 4.5
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198 1 -1 9 8 5.5
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199 1 1 9 9 4.5
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200 1 -1 9 9 5.5
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201 1 -1 9.28495 2.13839 8.88019
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202 1 1 4.99281 4.17459 9.83905
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203 1 -1 4.91265 6.89408 2.39989
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204 1 1 4.43647 3.68895 8.86086
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205 1 -1 0.659075 7.07271 0.179131
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206 1 1 7.791 3.40021 0.969703
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207 1 -1 1.18008 3.63874 7.28751
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208 1 1 8.51522 5.24681 6.37702
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209 1 -1 4.24226 9.60726 3.16084
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210 1 1 8.43745 8.23344 9.2883
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211 1 -1 8.48509 8.84988 9.43407
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212 1 1 2.81127 8.9903 0.00909212
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213 1 -1 6.38283 6.20858 9.92482
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214 1 1 4.59962 5.7925 7.52571
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215 1 -1 7.03797 7.09336 8.15957
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216 1 1 6.68103 8.04734 7.95661
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217 1 -1 2.531 8.47145 1.6209
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218 1 1 6.71915 8.79876 9.59581
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219 1 -1 4.96758 0.0381298 0.827927
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220 1 1 9.22955 1.04572 0.84722
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221 1 -1 2.3224 2.57084 8.07306
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222 1 1 1.94283 3.17375 3.92051
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223 1 -1 2.34735 1.91295 1.29127
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224 1 1 3.33928 3.30688 0.892089
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225 1 -1 1.19738 4.40402 8.70835
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226 1 1 7.44541 4.94803 8.28211
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227 1 -1 5.93272 1.18886 1.56518
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228 1 1 8.50709 8.70343 1.24939
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229 1 -1 5.54016 3.38865 8.61698
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230 1 1 9.47644 0.573085 3.05941
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231 1 -1 9.39695 4.46542 1.84205
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232 1 1 3.52268 5.60212 0.333999
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233 1 -1 3.69009 9.40954 6.10446
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234 1 1 3.96836 6.15307 7.57803
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235 1 -1 2.02535 0.0418407 3.21642
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236 1 1 2.97488 8.79711 8.33242
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237 1 -1 2.4122 1.79458 3.04173
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238 1 1 9.72355 3.67773 1.52435
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239 1 -1 8.55216 6.1623 1.53201
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240 1 1 4.98973 2.41459 9.84381
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241 1 -1 8.8901 5.9006 1.97649
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242 1 1 9.09932 2.23783 1.42554
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243 1 -1 6.70722 8.21769 1.21953
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244 1 1 6.83768 0.84508 3.25165
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245 1 -1 0.222115 3.07945 0.51825
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246 1 1 0.503918 9.34932 6.25278
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247 1 -1 0.803159 8.7017 9.46211
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248 1 1 4.88636 5.00147 9.65639
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249 1 -1 1.62258 0.767285 9.63596
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250 1 1 2.70143 3.01111 7.74859
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251 1 -1 4.41574 5.31824 0.538729
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252 1 1 1.64724 5.18097 3.59205
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253 1 -1 2.33672 3.21408 6.6081
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254 1 1 7.46603 1.53668 9.09844
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255 1 -1 3.61269 8.44556 6.99789
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256 1 1 6.95465 6.83045 9.31002
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257 1 -1 5.91831 9.01549 3.4626
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258 1 1 6.56503 8.42229 3.27105
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259 1 -1 4.50822 9.59753 3.47025
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260 1 1 4.17357 5.27384 7.34774
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261 1 -1 7.70968 6.5292 3.54779
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262 1 1 4.7977 4.94239 6.24947
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263 1 -1 9.24016 9.36994 6.71263
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264 1 1 7.36888 8.75922 0.52403
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265 1 -1 9.92895 5.87551 6.21586
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266 1 1 3.86308 6.71601 9.69083
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267 1 -1 8.90048 0.298719 0.573852
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268 1 1 6.58753 6.67768 1.83984
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269 1 -1 8.672 0.367497 2.21864
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270 1 1 3.44519 3.30359 6.52249
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271 1 -1 7.24717 3.25113 3.41567
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272 1 1 9.53447 5.81336 1.79208
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273 1 -1 1.01722 6.42534 0.715
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274 1 1 3.58808 4.92392 7.00979
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275 1 -1 1.21399 3.56951 6.34505
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276 1 1 3.50336 0.942722 2.76989
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277 1 -1 9.45475 6.06299 0.659023
|
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278 1 1 3.44464 4.03075 6.20179
|
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279 1 -1 0.949331 5.40183 8.51385
|
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280 1 1 6.41118 2.62135 2.31132
|
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281 1 -1 3.58837 9.78355 7.04966
|
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282 1 1 9.2267 3.19593 2.10384
|
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283 1 -1 1.83092 2.35627 3.93061
|
||||
284 1 1 4.97203 4.92287 1.8049
|
||||
285 1 -1 7.4097 4.757 8.604
|
||||
286 1 1 0.746575 7.69038 0.89134
|
||||
287 1 -1 8.54862 6.59135 2.18888
|
||||
288 1 1 2.18747 4.82994 0.761718
|
||||
289 1 -1 5.71622 2.51116 6.85522
|
||||
290 1 1 6.95554 1.83187 8.31157
|
||||
291 1 -1 7.31818 6.60081 2.63208
|
||||
292 1 1 0.744495 2.73429 9.86022
|
||||
293 1 -1 5.1573 8.70962 2.53418
|
||||
294 1 1 2.40385 1.54057 1.9297
|
||||
295 1 -1 3.42609 2.25856 2.28437
|
||||
296 1 1 6.66173 3.70851 9.70052
|
||||
297 1 -1 7.88966 1.4343 8.91223
|
||||
298 1 1 3.91118 5.22253 6.29642
|
||||
299 1 -1 9.17618 3.98313 9.82158
|
||||
300 1 1 4.95424 5.93521 1.3652
|
||||
1016
examples/USER/scafacos/data.hammersley_shphere
Normal file
1016
examples/USER/scafacos/data.hammersley_shphere
Normal file
File diff suppressed because it is too large
Load Diff
31
examples/USER/scafacos/in.scafacos.cw.ewald
Normal file
31
examples/USER/scafacos/in.scafacos.cw.ewald
Normal file
@ -0,0 +1,31 @@
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|
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units lj
|
||||
atom_style charge
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||||
|
||||
read_data data.cloud_wall
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||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos ewald 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
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||||
37
examples/USER/scafacos/in.scafacos.cw.fmm
Normal file
37
examples/USER/scafacos/in.scafacos.cw.fmm
Normal file
@ -0,0 +1,37 @@
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||||
units lj
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||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
kspace_style scafacos fmm 1.0e-3
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
31
examples/USER/scafacos/in.scafacos.cw.p2nfft
Normal file
31
examples/USER/scafacos/in.scafacos.cw.p2nfft
Normal file
@ -0,0 +1,31 @@
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
37
examples/USER/scafacos/in.scafacos.ewald
Normal file
37
examples/USER/scafacos/in.scafacos.ewald
Normal file
@ -0,0 +1,37 @@
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
|
||||
replicate 8 8 8
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos ewald 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
37
examples/USER/scafacos/in.scafacos.fmm
Normal file
37
examples/USER/scafacos/in.scafacos.fmm
Normal file
@ -0,0 +1,37 @@
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
|
||||
replicate 8 8 8
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
34
examples/USER/scafacos/in.scafacos.hsph.direct
Normal file
34
examples/USER/scafacos/in.scafacos.hsph.direct
Normal file
@ -0,0 +1,34 @@
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos direct 0.001
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
run 20
|
||||
37
examples/USER/scafacos/in.scafacos.hsph.fmm
Normal file
37
examples/USER/scafacos/in.scafacos.hsph.fmm
Normal file
@ -0,0 +1,37 @@
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
36
examples/USER/scafacos/in.scafacos.hsph.p2nfft
Normal file
36
examples/USER/scafacos/in.scafacos.hsph.p2nfft
Normal file
@ -0,0 +1,36 @@
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance potential
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
37
examples/USER/scafacos/in.scafacos.p2nfft
Normal file
37
examples/USER/scafacos/in.scafacos.p2nfft
Normal file
@ -0,0 +1,37 @@
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
|
||||
replicate 8 8 8
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16
Normal file
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos ewald 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver ewald ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.313 | 3.501 | 3.689 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49647271 0 0.49647271 0
|
||||
10 300 0.061254978 0.014582562 0.44286522 0.02180093 0.46466616 0
|
||||
20 300 0.12240911 0.058693359 0.37869251 0.087746571 0.46643909 0
|
||||
30 300 0.18348265 0.13468789 0.26730177 0.2013584 0.46866017 0
|
||||
40 300 0.24441123 0.50949535 0.083356437 0.76169555 0.84505198 0
|
||||
50 300 0.30493236 1.1731116 -0.055261984 1.7538018 1.6985399 0
|
||||
60 300 0.36615515 1.3589639 -0.33351524 2.031651 1.6981358 0
|
||||
70 300 0.42717433 1.6482648 -0.76570045 2.4641559 1.6984554 0
|
||||
80 300 0.48137259 2.8640899 -2.4038488 4.2818144 1.8779656 0
|
||||
90 300 0.5323379 93.168442 -2.5911448 139.28682 136.69568 0
|
||||
100 300 0.5756321 94.146897 -1.3480439 140.74961 139.40157 0
|
||||
Loop time of 0.575655 on 16 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 75045.007 tau/day, 173.715 timesteps/s
|
||||
98.7% CPU use with 16 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2159e-05 | 1.739e-05 | 2.3127e-05 | 0.0 | 0.00
|
||||
Kspace | 0.57008 | 0.57086 | 0.57137 | 0.1 | 99.17
|
||||
Neigh | 0.00025606 | 0.00061357 | 0.001369 | 0.0 | 0.11
|
||||
Comm | 0.0023558 | 0.0027267 | 0.003104 | 0.4 | 0.47
|
||||
Output | 0.00029898 | 0.00032344 | 0.00037599 | 0.0 | 0.06
|
||||
Modify | 8.2493e-05 | 0.00014143 | 0.00021815 | 0.0 | 0.02
|
||||
Other | | 0.0009701 | | | 0.17
|
||||
|
||||
Nlocal: 18.75 ave 39 max 6 min
|
||||
Histogram: 6 1 1 0 1 2 2 1 1 1
|
||||
Nghost: 122.812 ave 195 max 63 min
|
||||
Histogram: 8 0 0 0 0 0 0 1 3 4
|
||||
Neighs: 160.625 ave 598 max 13 min
|
||||
Histogram: 8 2 1 1 1 0 0 2 0 1
|
||||
|
||||
Total # of neighbors = 2570
|
||||
Ave neighs/atom = 8.56667
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 16
|
||||
Total wall time: 0:00:00
|
||||
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8
Normal file
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos ewald 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver ewald ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.317 | 3.317 | 3.317 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49647271 0 0.49647271 0
|
||||
10 300 0.067519665 0.014718629 0.45088339 0.02200435 0.47288774 0
|
||||
20 300 0.13502312 0.05922597 0.38470912 0.088542825 0.47325194 0
|
||||
30 300 0.20248008 0.13587829 0.27058048 0.20313804 0.47371852 0
|
||||
40 300 0.26985955 0.51353118 0.088432648 0.76772911 0.85616176 0
|
||||
50 300 0.33801103 1.1760001 -0.058088247 1.7581201 1.7000319 0
|
||||
60 300 0.40665984 1.3627885 -0.33736672 2.0373688 1.7000021 0
|
||||
70 300 0.47533679 1.6529365 -0.77082139 2.4711401 1.7003187 0
|
||||
80 300 0.54396391 2.9569837 -2.4624654 4.4206907 1.9582253 0
|
||||
90 300 0.61429667 81.642726 -2.5370215 122.05588 119.51885 0
|
||||
100 300 0.68513632 85.047974 -1.128107 127.14672 126.01861 0
|
||||
Loop time of 0.685155 on 8 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 63051.442 tau/day, 145.952 timesteps/s
|
||||
99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.0967e-05 | 1.4216e-05 | 1.8358e-05 | 0.0 | 0.00
|
||||
Kspace | 0.67942 | 0.67981 | 0.6803 | 0.0 | 99.22
|
||||
Neigh | 0.00073242 | 0.0010653 | 0.0015635 | 0.8 | 0.16
|
||||
Comm | 0.0029492 | 0.0031102 | 0.0033047 | 0.2 | 0.45
|
||||
Output | 0.00021768 | 0.00023454 | 0.00028443 | 0.0 | 0.03
|
||||
Modify | 0.00016046 | 0.00018132 | 0.00019431 | 0.0 | 0.03
|
||||
Other | | 0.0007433 | | | 0.11
|
||||
|
||||
Nlocal: 37.5 ave 46 max 31 min
|
||||
Histogram: 2 0 0 2 1 0 2 0 0 1
|
||||
Nghost: 203.875 ave 212 max 192 min
|
||||
Histogram: 1 0 1 0 0 2 1 0 0 3
|
||||
Neighs: 321.625 ave 599 max 112 min
|
||||
Histogram: 1 2 0 1 1 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 2573
|
||||
Ave neighs/atom = 8.57667
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 16
|
||||
Total wall time: 0:00:00
|
||||
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1
Normal file
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1
Normal file
@ -0,0 +1,99 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
kspace_style scafacos fmm 1.0e-3
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.34 | 3.34 | 3.34 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49646402 0 0.49646402 0
|
||||
10 300 0.036603451 0.015455559 0.47335833 0.02310606 0.49646439 0
|
||||
20 300 0.073534727 0.06229069 0.40334177 0.093124582 0.49646635 0
|
||||
30 300 0.10984373 0.14310163 0.28254277 0.21393694 0.49647971 0
|
||||
40 300 0.14610171 0.52929788 0.089669015 0.79130033 0.88096934 0
|
||||
50 300 0.18255496 1.1963022 -0.082792461 1.7884718 1.7056794 0
|
||||
60 300 0.2194376 1.3928167 -0.37659239 2.082261 1.7056686 0
|
||||
70 300 0.25588369 1.7069009 -0.84571914 2.5518169 1.7060978 0
|
||||
80 300 0.29101205 15.358343 -3.368063 22.960722 19.592659 0
|
||||
90 300 0.32697225 42.280432 -2.1623864 63.209247 61.04686 0
|
||||
100 300 0.36395645 41.48079 -0.89904529 62.013782 61.114736 0
|
||||
Loop time of 0.363968 on 1 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 118691.709 tau/day, 274.749 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2875e-05 | 1.2875e-05 | 1.2875e-05 | 0.0 | 0.00
|
||||
Kspace | 0.35715 | 0.35715 | 0.35715 | 0.0 | 98.13
|
||||
Neigh | 0.0039768 | 0.0039768 | 0.0039768 | 0.0 | 1.09
|
||||
Comm | 0.0012023 | 0.0012023 | 0.0012023 | 0.0 | 0.33
|
||||
Output | 0.0001502 | 0.0001502 | 0.0001502 | 0.0 | 0.04
|
||||
Modify | 0.0009768 | 0.0009768 | 0.0009768 | 0.0 | 0.27
|
||||
Other | | 0.0005031 | | | 0.14
|
||||
|
||||
Nlocal: 300 ave 300 max 300 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 374 ave 374 max 374 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2459 ave 2459 max 2459 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2459
|
||||
Ave neighs/atom = 8.19667
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16
Normal file
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16
Normal file
@ -0,0 +1,99 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
kspace_style scafacos fmm 1.0e-3
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.313 | 3.501 | 3.689 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49646402 0 0.49646402 0
|
||||
10 300 0.018873215 0.015455559 0.47335833 0.02310606 0.49646439 0
|
||||
20 300 0.035197735 0.06229069 0.40334177 0.093124582 0.49646635 0
|
||||
30 300 0.051513195 0.14310163 0.28254277 0.21393694 0.49647971 0
|
||||
40 300 0.067400217 0.52929788 0.089669015 0.79130033 0.88096934 0
|
||||
50 300 0.083569527 1.1963022 -0.082792461 1.7884718 1.7056794 0
|
||||
60 300 0.099931955 1.3928167 -0.37659239 2.082261 1.7056686 0
|
||||
70 300 0.11602688 1.7069009 -0.84571914 2.5518169 1.7060978 0
|
||||
80 300 0.13271379 15.358343 -3.368063 22.960722 19.592659 0
|
||||
90 300 0.15055513 42.280432 -2.1623864 63.209247 61.04686 0
|
||||
100 300 0.16817498 41.48079 -0.89904529 62.013782 61.114736 0
|
||||
Loop time of 0.168194 on 16 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 256846.586 tau/day, 594.552 timesteps/s
|
||||
97.7% CPU use with 16 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.4544e-05 | 2.0206e-05 | 2.6941e-05 | 0.0 | 0.01
|
||||
Kspace | 0.16313 | 0.16373 | 0.16423 | 0.1 | 97.34
|
||||
Neigh | 0.00016737 | 0.00039591 | 0.00084519 | 0.0 | 0.24
|
||||
Comm | 0.0021157 | 0.0026083 | 0.0032525 | 0.7 | 1.55
|
||||
Output | 0.00026298 | 0.00030228 | 0.00035977 | 0.0 | 0.18
|
||||
Modify | 0.00010705 | 0.00015062 | 0.00020647 | 0.0 | 0.09
|
||||
Other | | 0.0009913 | | | 0.59
|
||||
|
||||
Nlocal: 18.75 ave 36 max 6 min
|
||||
Histogram: 4 3 1 0 0 1 2 1 2 2
|
||||
Nghost: 127 ave 196 max 71 min
|
||||
Histogram: 8 0 0 0 0 0 0 1 6 1
|
||||
Neighs: 153.688 ave 491 max 10 min
|
||||
Histogram: 8 1 1 1 1 1 0 0 0 3
|
||||
|
||||
Total # of neighbors = 2459
|
||||
Ave neighs/atom = 8.19667
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2
Normal file
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2
Normal file
@ -0,0 +1,99 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
kspace_style scafacos fmm 1.0e-3
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.354 | 3.354 | 3.355 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49646402 0 0.49646402 0
|
||||
10 300 0.021326542 0.015455559 0.47335833 0.02310606 0.49646439 0
|
||||
20 300 0.043129683 0.06229069 0.40334177 0.093124582 0.49646635 0
|
||||
30 300 0.064425707 0.14310163 0.28254277 0.21393694 0.49647971 0
|
||||
40 300 0.085822344 0.52929788 0.089669015 0.79130033 0.88096934 0
|
||||
50 300 0.10737753 1.1963022 -0.082792461 1.7884718 1.7056794 0
|
||||
60 300 0.12947297 1.3928167 -0.37659239 2.082261 1.7056686 0
|
||||
70 300 0.15108895 1.7069009 -0.84571914 2.5518169 1.7060978 0
|
||||
80 300 0.17378163 15.358343 -3.368063 22.960722 19.592659 0
|
||||
90 300 0.19809985 42.280432 -2.1623864 63.209247 61.04686 0
|
||||
100 300 0.22268319 41.48079 -0.89904529 62.013782 61.114736 0
|
||||
Loop time of 0.222696 on 2 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 193986.156 tau/day, 449.042 timesteps/s
|
||||
98.4% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1683e-05 | 1.5378e-05 | 1.9073e-05 | 0.0 | 0.01
|
||||
Kspace | 0.21627 | 0.2168 | 0.21734 | 0.1 | 97.35
|
||||
Neigh | 0.0016344 | 0.0021609 | 0.0026875 | 1.1 | 0.97
|
||||
Comm | 0.0022857 | 0.0023286 | 0.0023715 | 0.1 | 1.05
|
||||
Output | 0.00015521 | 0.00019228 | 0.00022936 | 0.0 | 0.09
|
||||
Modify | 0.00052834 | 0.00054049 | 0.00055265 | 0.0 | 0.24
|
||||
Other | | 0.0006541 | | | 0.29
|
||||
|
||||
Nlocal: 150 ave 159 max 141 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 392 ave 395 max 389 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 1229.5 ave 1773 max 686 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2459
|
||||
Ave neighs/atom = 8.19667
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4
Normal file
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4
Normal file
@ -0,0 +1,99 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
kspace_style scafacos fmm 1.0e-3
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.333 | 3.333 | 3.333 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49646402 0 0.49646402 0
|
||||
10 300 0.017563343 0.015455559 0.47335833 0.02310606 0.49646439 0
|
||||
20 300 0.034884214 0.06229069 0.40334177 0.093124582 0.49646635 0
|
||||
30 300 0.052014828 0.14310163 0.28254277 0.21393694 0.49647971 0
|
||||
40 300 0.069101095 0.52929788 0.089669015 0.79130033 0.88096934 0
|
||||
50 300 0.085633039 1.1963022 -0.082792461 1.7884718 1.7056794 0
|
||||
60 300 0.10165119 1.3928167 -0.37659239 2.082261 1.7056686 0
|
||||
70 300 0.11729789 1.7069009 -0.84571914 2.5518169 1.7060978 0
|
||||
80 300 0.1342802 15.358343 -3.368063 22.960722 19.592659 0
|
||||
90 300 0.15266848 42.280432 -2.1623864 63.209247 61.04686 0
|
||||
100 300 0.17004442 41.48079 -0.89904529 62.013782 61.114736 0
|
||||
Loop time of 0.170072 on 4 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 254010.216 tau/day, 587.987 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5497e-05 | 1.6868e-05 | 1.9789e-05 | 0.0 | 0.01
|
||||
Kspace | 0.16417 | 0.16472 | 0.16507 | 0.1 | 96.86
|
||||
Neigh | 0.00082564 | 0.0012031 | 0.0015855 | 0.9 | 0.71
|
||||
Comm | 0.0026572 | 0.0029335 | 0.003197 | 0.4 | 1.72
|
||||
Output | 0.00019169 | 0.00021791 | 0.00026536 | 0.0 | 0.13
|
||||
Modify | 0.00031304 | 0.00032955 | 0.00035334 | 0.0 | 0.19
|
||||
Other | | 0.0006474 | | | 0.38
|
||||
|
||||
Nlocal: 75 ave 81 max 70 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 282.5 ave 290 max 274 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Neighs: 614.75 ave 981 max 285 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 2459
|
||||
Ave neighs/atom = 8.19667
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8
Normal file
99
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8
Normal file
@ -0,0 +1,99 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
kspace_style scafacos fmm 1.0e-3
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.317 | 3.317 | 3.317 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49646402 0 0.49646402 0
|
||||
10 300 0.016258478 0.015455559 0.47335833 0.02310606 0.49646439 0
|
||||
20 300 0.031442165 0.06229069 0.40334177 0.093124582 0.49646635 0
|
||||
30 300 0.046462774 0.14310163 0.28254277 0.21393694 0.49647971 0
|
||||
40 300 0.061176538 0.52929788 0.089669015 0.79130033 0.88096934 0
|
||||
50 300 0.076244354 1.1963022 -0.082792461 1.7884718 1.7056794 0
|
||||
60 300 0.091396809 1.3928167 -0.37659239 2.082261 1.7056686 0
|
||||
70 300 0.10625911 1.7069009 -0.84571914 2.5518169 1.7060978 0
|
||||
80 300 0.1204896 15.358343 -3.368063 22.960722 19.592659 0
|
||||
90 300 0.13657618 42.280432 -2.1623864 63.209247 61.04686 0
|
||||
100 300 0.15163732 41.48079 -0.89904529 62.013782 61.114736 0
|
||||
Loop time of 0.151654 on 8 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 284858.554 tau/day, 659.395 timesteps/s
|
||||
97.7% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3828e-05 | 1.6987e-05 | 1.955e-05 | 0.0 | 0.01
|
||||
Kspace | 0.14633 | 0.14689 | 0.14725 | 0.1 | 96.86
|
||||
Neigh | 0.00047135 | 0.00067887 | 0.00094771 | 0.0 | 0.45
|
||||
Comm | 0.0027649 | 0.0029218 | 0.0032592 | 0.3 | 1.93
|
||||
Output | 0.00022578 | 0.00024724 | 0.00030136 | 0.0 | 0.16
|
||||
Modify | 0.00018954 | 0.00021681 | 0.0002358 | 0.0 | 0.14
|
||||
Other | | 0.0006794 | | | 0.45
|
||||
|
||||
Nlocal: 37.5 ave 45 max 31 min
|
||||
Histogram: 1 1 1 1 1 0 1 0 1 1
|
||||
Nghost: 200 ave 209 max 189 min
|
||||
Histogram: 1 0 0 0 1 4 0 0 0 2
|
||||
Neighs: 307.375 ave 514 max 115 min
|
||||
Histogram: 2 1 0 1 1 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 2459
|
||||
Ave neighs/atom = 8.19667
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1
Normal file
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.34 | 3.34 | 3.34 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49683273 0 0.49683273 0
|
||||
10 300 0.082981586 0.015479312 0.47369009 0.023141571 0.49683166 0
|
||||
20 300 0.16677213 0.062386358 0.40356181 0.093267605 0.49682941 0
|
||||
30 300 0.2506392 0.14331637 0.2825636 0.21425798 0.49682157 0
|
||||
40 300 0.33466673 0.53041843 0.089505208 0.79297556 0.88248077 0
|
||||
50 300 0.41812825 1.1948397 -0.083317439 1.7862853 1.7029679 0
|
||||
60 300 0.50167894 1.3915614 -0.37745551 2.0803842 1.7029287 0
|
||||
70 300 0.58574796 1.7061978 -0.84746071 2.5507657 1.703305 0
|
||||
80 300 0.6700325 20.692093 -3.32971 30.93468 27.60497 0
|
||||
90 300 0.75608635 48.999403 -2.1632167 73.254107 71.090891 0
|
||||
100 300 0.84190726 51.199785 -0.81127924 76.543678 75.732399 0
|
||||
Loop time of 0.841921 on 1 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 51311.251 tau/day, 118.776 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1206e-05 | 1.1206e-05 | 1.1206e-05 | 0.0 | 0.00
|
||||
Kspace | 0.835 | 0.835 | 0.835 | 0.0 | 99.18
|
||||
Neigh | 0.0040102 | 0.0040102 | 0.0040102 | 0.0 | 0.48
|
||||
Comm | 0.0012431 | 0.0012431 | 0.0012431 | 0.0 | 0.15
|
||||
Output | 0.0001545 | 0.0001545 | 0.0001545 | 0.0 | 0.02
|
||||
Modify | 0.0010202 | 0.0010202 | 0.0010202 | 0.0 | 0.12
|
||||
Other | | 0.000484 | | | 0.06
|
||||
|
||||
Nlocal: 300 ave 300 max 300 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 381 ave 381 max 381 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2461 ave 2461 max 2461 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2461
|
||||
Ave neighs/atom = 8.20333
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16
Normal file
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.313 | 3.501 | 3.689 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49683273 0 0.49683273 0
|
||||
10 300 0.029647827 0.015479312 0.47369009 0.023141571 0.49683166 0
|
||||
20 300 0.059298515 0.062386358 0.40356181 0.093267605 0.49682941 0
|
||||
30 300 0.088926077 0.14331637 0.2825636 0.21425798 0.49682157 0
|
||||
40 300 0.11850166 0.53041843 0.089505208 0.79297556 0.88248077 0
|
||||
50 300 0.14820433 1.1948397 -0.083317439 1.7862853 1.7029679 0
|
||||
60 300 0.17807317 1.3915614 -0.37745551 2.0803842 1.7029287 0
|
||||
70 300 0.20803642 1.7061978 -0.84746071 2.5507657 1.703305 0
|
||||
80 300 0.23797083 20.692093 -3.32971 30.93468 27.60497 0
|
||||
90 300 0.26835561 48.999403 -2.1632167 73.254107 71.090891 0
|
||||
100 300 0.29766583 51.199785 -0.81127924 76.543678 75.732399 0
|
||||
Loop time of 0.297693 on 16 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 145116.000 tau/day, 335.917 timesteps/s
|
||||
98.8% CPU use with 16 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1683e-05 | 1.6928e-05 | 2.4557e-05 | 0.0 | 0.01
|
||||
Kspace | 0.29245 | 0.29325 | 0.29366 | 0.1 | 98.51
|
||||
Neigh | 0.00017214 | 0.00042973 | 0.0010228 | 0.0 | 0.14
|
||||
Comm | 0.0021176 | 0.0024613 | 0.0028479 | 0.5 | 0.83
|
||||
Output | 0.00028467 | 0.00033538 | 0.00041103 | 0.0 | 0.11
|
||||
Modify | 8.893e-05 | 0.00015014 | 0.00027537 | 0.0 | 0.05
|
||||
Other | | 0.001048 | | | 0.35
|
||||
|
||||
Nlocal: 18.75 ave 33 max 6 min
|
||||
Histogram: 2 6 0 0 0 0 2 1 2 3
|
||||
Nghost: 128.875 ave 198 max 71 min
|
||||
Histogram: 7 1 0 0 0 0 0 1 5 2
|
||||
Neighs: 153.812 ave 490 max 14 min
|
||||
Histogram: 8 0 3 0 1 1 0 0 1 2
|
||||
|
||||
Total # of neighbors = 2461
|
||||
Ave neighs/atom = 8.20333
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2
Normal file
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.354 | 3.354 | 3.355 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49683273 0 0.49683273 0
|
||||
10 300 0.049199581 0.015479312 0.47369009 0.023141571 0.49683166 0
|
||||
20 300 0.09860301 0.062386358 0.40356181 0.093267605 0.49682941 0
|
||||
30 300 0.14826894 0.14331637 0.2825636 0.21425798 0.49682157 0
|
||||
40 300 0.19769144 0.53041843 0.089505208 0.79297556 0.88248077 0
|
||||
50 300 0.24735355 1.1948397 -0.083317439 1.7862853 1.7029679 0
|
||||
60 300 0.29692888 1.3915614 -0.37745551 2.0803842 1.7029287 0
|
||||
70 300 0.34639764 1.7061978 -0.84746071 2.5507657 1.703305 0
|
||||
80 300 0.39633083 20.692093 -3.32971 30.93468 27.60497 0
|
||||
90 300 0.44779778 48.999403 -2.1632167 73.254107 71.090891 0
|
||||
100 300 0.49988627 51.199785 -0.81127924 76.543678 75.732399 0
|
||||
Loop time of 0.499909 on 2 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 86415.782 tau/day, 200.037 timesteps/s
|
||||
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.0599e-06 | 1.3709e-05 | 1.8358e-05 | 0.0 | 0.00
|
||||
Kspace | 0.49314 | 0.49365 | 0.49416 | 0.1 | 98.75
|
||||
Neigh | 0.0016146 | 0.0021083 | 0.0026021 | 1.1 | 0.42
|
||||
Comm | 0.002754 | 0.0028276 | 0.0029013 | 0.1 | 0.57
|
||||
Output | 0.00015783 | 0.00019348 | 0.00022912 | 0.0 | 0.04
|
||||
Modify | 0.00049257 | 0.00049472 | 0.00049686 | 0.0 | 0.10
|
||||
Other | | 0.0006217 | | | 0.12
|
||||
|
||||
Nlocal: 150 ave 157 max 143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 399 ave 402 max 396 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 1230.5 ave 1756 max 705 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2461
|
||||
Ave neighs/atom = 8.20333
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4
Normal file
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.333 | 3.333 | 3.333 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49683273 0 0.49683273 0
|
||||
10 300 0.031973124 0.015479312 0.47369009 0.023141571 0.49683166 0
|
||||
20 300 0.064628601 0.062386358 0.40356181 0.093267605 0.49682941 0
|
||||
30 300 0.096747875 0.14331637 0.2825636 0.21425798 0.49682157 0
|
||||
40 300 0.12864041 0.53041843 0.089505208 0.79297556 0.88248077 0
|
||||
50 300 0.161134 1.1948397 -0.083317439 1.7862853 1.7029679 0
|
||||
60 300 0.19359422 1.3915614 -0.37745551 2.0803842 1.7029287 0
|
||||
70 300 0.22573543 1.7061978 -0.84746071 2.5507657 1.703305 0
|
||||
80 300 0.25922132 20.692093 -3.32971 30.93468 27.60497 0
|
||||
90 300 0.29452014 48.999403 -2.1632167 73.254107 71.090891 0
|
||||
100 300 0.33031607 51.199785 -0.81127924 76.543678 75.732399 0
|
||||
Loop time of 0.330333 on 4 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 130777.056 tau/day, 302.725 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.0014e-05 | 1.3471e-05 | 1.5497e-05 | 0.0 | 0.00
|
||||
Kspace | 0.32504 | 0.3255 | 0.3258 | 0.1 | 98.54
|
||||
Neigh | 0.00083303 | 0.0011883 | 0.0015609 | 0.8 | 0.36
|
||||
Comm | 0.0024087 | 0.0025436 | 0.0026674 | 0.2 | 0.77
|
||||
Output | 0.00017405 | 0.00020278 | 0.00024986 | 0.0 | 0.06
|
||||
Modify | 0.00028658 | 0.00031012 | 0.00033331 | 0.0 | 0.09
|
||||
Other | | 0.0005748 | | | 0.17
|
||||
|
||||
Nlocal: 75 ave 81 max 69 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 287 ave 296 max 278 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 615.25 ave 964 max 286 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 2461
|
||||
Ave neighs/atom = 8.20333
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8
Normal file
92
examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.cloud_wall
|
||||
orthogonal box = (0 0 0) to (10 10 10)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
300 atoms
|
||||
|
||||
velocity all set 0.0 0.0 0.0 mom no
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
|
||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul
|
||||
|
||||
run_style verlet
|
||||
|
||||
#dump simple all custom 1000 id x y z vx vy vz
|
||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||
#dump_modify dmpvtk pad 7
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.317 | 3.317 | 3.317 Mbytes
|
||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul
|
||||
0 300 0 0 0.49683273 0 0.49683273 0
|
||||
10 300 0.023941755 0.015479312 0.47369009 0.023141571 0.49683166 0
|
||||
20 300 0.047938108 0.062386358 0.40356181 0.093267605 0.49682941 0
|
||||
30 300 0.071953773 0.14331637 0.2825636 0.21425798 0.49682157 0
|
||||
40 300 0.095941782 0.53041843 0.089505208 0.79297556 0.88248077 0
|
||||
50 300 0.12011361 1.1948397 -0.083317439 1.7862853 1.7029679 0
|
||||
60 300 0.14433384 1.3915614 -0.37745551 2.0803842 1.7029287 0
|
||||
70 300 0.16875505 1.7061978 -0.84746071 2.5507657 1.703305 0
|
||||
80 300 0.193331 20.692093 -3.32971 30.93468 27.60497 0
|
||||
90 300 0.21844888 48.999403 -2.1632167 73.254107 71.090891 0
|
||||
100 300 0.24417853 51.199785 -0.81127924 76.543678 75.732399 0
|
||||
Loop time of 0.244198 on 8 procs for 100 steps with 300 atoms
|
||||
|
||||
Performance: 176905.349 tau/day, 409.503 timesteps/s
|
||||
99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.7752e-06 | 1.4246e-05 | 1.955e-05 | 0.0 | 0.01
|
||||
Kspace | 0.23946 | 0.23972 | 0.24009 | 0.0 | 98.17
|
||||
Neigh | 0.00049043 | 0.00071204 | 0.00095773 | 0.0 | 0.29
|
||||
Comm | 0.0025063 | 0.0026675 | 0.0027597 | 0.2 | 1.09
|
||||
Output | 0.00019646 | 0.00021604 | 0.00026321 | 0.0 | 0.09
|
||||
Modify | 0.00017905 | 0.0001913 | 0.00020766 | 0.0 | 0.08
|
||||
Other | | 0.0006773 | | | 0.28
|
||||
|
||||
Nlocal: 37.5 ave 42 max 33 min
|
||||
Histogram: 2 1 0 1 0 0 1 0 1 2
|
||||
Nghost: 202.25 ave 212 max 194 min
|
||||
Histogram: 1 0 2 1 0 2 0 1 0 1
|
||||
Neighs: 307.625 ave 505 max 129 min
|
||||
Histogram: 3 0 0 1 1 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 2461
|
||||
Ave neighs/atom = 8.20333
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000503302 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos ewald 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver ewald ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.401 | 3.401 | 3.401 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87413076 0 1.3753199 1.4996338
|
||||
10 1.5001167 -0.84976141 0 1.3998642 1.4997504
|
||||
20 1.5002402 -0.84977464 0 1.4000363 1.499874
|
||||
30 1.5003611 -0.84978325 0 1.4002089 1.4999948
|
||||
40 1.5004736 -0.84977869 0 1.4003823 1.5001073
|
||||
50 1.5005703 -0.8497468 0 1.4005591 1.5002039
|
||||
60 1.5006418 -0.84967646 0 1.4007366 1.5002754
|
||||
70 1.5006785 -0.84955497 0 1.4009132 1.5003121
|
||||
80 1.5006711 -0.849369 0 1.4010881 1.5003047
|
||||
90 1.500611 -0.84910811 0 1.4012589 1.5002446
|
||||
100 1.5004911 -0.84870167 0 1.4014854 1.5001247
|
||||
Loop time of 46.4857 on 16 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 929.317 tau/day, 2.151 timesteps/s
|
||||
99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00023437 | 0.00024788 | 0.00026894 | 0.0 | 0.00
|
||||
Kspace | 46.476 | 46.476 | 46.476 | 0.0 | 99.98
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0062859 | 0.0067717 | 0.0072649 | 0.3 | 0.01
|
||||
Output | 0.0004127 | 0.00044075 | 0.00050807 | 0.0 | 0.00
|
||||
Modify | 0.00099325 | 0.0010343 | 0.0010939 | 0.1 | 0.00
|
||||
Other | | 0.001459 | | | 0.00
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1265 ave 1265 max 1265 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4096 ave 4096 max 4096 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:47
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000281811 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos ewald 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver ewald ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.416 | 3.416 | 3.416 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87413076 0 1.3753199 1.4996338
|
||||
10 1.5001095 -0.85040058 0 1.3992143 1.4997433
|
||||
20 1.5002258 -0.85039456 0 1.3993947 1.4998595
|
||||
30 1.5003395 -0.85038368 0 1.3995761 1.4999732
|
||||
40 1.5004452 -0.85035944 0 1.3997589 1.5000789
|
||||
50 1.5005354 -0.85030783 0 1.3999457 1.500169
|
||||
60 1.5006008 -0.85021779 0 1.4001339 1.5002344
|
||||
70 1.500632 -0.8500769 0 1.4003215 1.5002656
|
||||
80 1.5006197 -0.84987187 0 1.4005081 1.5002533
|
||||
90 1.5005554 -0.84959251 0 1.400691 1.500189
|
||||
100 1.500432 -0.84916846 0 1.4009301 1.5000657
|
||||
Loop time of 86.1477 on 8 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 501.464 tau/day, 1.161 timesteps/s
|
||||
99.9% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.000314 | 0.00033289 | 0.00035048 | 0.0 | 0.00
|
||||
Kspace | 86.136 | 86.136 | 86.136 | 0.0 | 99.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0069821 | 0.0073864 | 0.0077834 | 0.3 | 0.01
|
||||
Output | 0.00038719 | 0.00041264 | 0.00047517 | 0.0 | 0.00
|
||||
Modify | 0.0018711 | 0.0019454 | 0.0020905 | 0.1 | 0.00
|
||||
Other | | 0.001762 | | | 0.00
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1685 ave 1685 max 1685 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8192 ave 8192 max 8192 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:28
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000584364 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.723 | 3.723 | 3.723 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87378819 0 1.3756625 1.4996338
|
||||
10 1.5000004 -0.87378882 0 1.3756625 1.4996342
|
||||
20 1.4999998 -0.87378782 0 1.3756625 1.4996336
|
||||
30 1.4999934 -0.87377823 0 1.3756625 1.4996272
|
||||
40 1.4999745 -0.87374997 0 1.3756625 1.4996083
|
||||
50 1.4999347 -0.87369019 0 1.3756625 1.4995685
|
||||
60 1.4998637 -0.87358381 0 1.3756625 1.4994975
|
||||
70 1.4997506 -0.87341428 0 1.3756624 1.4993845
|
||||
80 1.4995842 -0.87316464 0 1.3756624 1.499218
|
||||
90 1.4993536 -0.87281897 0 1.3756624 1.4989876
|
||||
100 1.4990503 -0.87236411 0 1.3756624 1.4986843
|
||||
Loop time of 5.26537 on 1 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 8204.550 tau/day, 18.992 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0011349 | 0.0011349 | 0.0011349 | 0.0 | 0.02
|
||||
Kspace | 5.2375 | 5.2375 | 5.2375 | 0.0 | 99.47
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0090225 | 0.0090225 | 0.0090225 | 0.0 | 0.17
|
||||
Output | 0.0004127 | 0.0004127 | 0.0004127 | 0.0 | 0.01
|
||||
Modify | 0.012851 | 0.012851 | 0.012851 | 0.0 | 0.24
|
||||
Other | | 0.004441 | | | 0.08
|
||||
|
||||
Nlocal: 4096 ave 4096 max 4096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5165 ave 5165 max 5165 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 65536 ave 65536 max 65536 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000507593 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.401 | 3.401 | 3.401 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87378819 0 1.3756625 1.4996338
|
||||
10 1.5000004 -0.87378882 0 1.3756625 1.4996342
|
||||
20 1.4999998 -0.87378782 0 1.3756625 1.4996336
|
||||
30 1.4999934 -0.87377823 0 1.3756625 1.4996272
|
||||
40 1.4999745 -0.87374997 0 1.3756625 1.4996083
|
||||
50 1.4999347 -0.87369019 0 1.3756625 1.4995685
|
||||
60 1.4998637 -0.87358381 0 1.3756625 1.4994975
|
||||
70 1.4997506 -0.87341428 0 1.3756624 1.4993845
|
||||
80 1.4995842 -0.87316464 0 1.3756624 1.499218
|
||||
90 1.4993536 -0.87281897 0 1.3756624 1.4989876
|
||||
100 1.4990503 -0.87236411 0 1.3756624 1.4986843
|
||||
Loop time of 0.570389 on 16 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 75737.813 tau/day, 175.319 timesteps/s
|
||||
99.3% CPU use with 16 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00024104 | 0.00025283 | 0.00029206 | 0.0 | 0.04
|
||||
Kspace | 0.56153 | 0.56176 | 0.56189 | 0.0 | 98.49
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0055203 | 0.0057825 | 0.0061858 | 0.2 | 1.01
|
||||
Output | 0.00038505 | 0.00040831 | 0.00048184 | 0.0 | 0.07
|
||||
Modify | 0.00096965 | 0.00099662 | 0.0010159 | 0.0 | 0.17
|
||||
Other | | 0.001192 | | | 0.21
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1265 ave 1265 max 1265 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4096 ave 4096 max 4096 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000455141 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.634 | 3.634 | 3.634 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87378819 0 1.3756625 1.4996338
|
||||
10 1.5000004 -0.87378882 0 1.3756625 1.4996342
|
||||
20 1.4999998 -0.87378782 0 1.3756625 1.4996336
|
||||
30 1.4999934 -0.87377823 0 1.3756625 1.4996272
|
||||
40 1.4999745 -0.87374997 0 1.3756625 1.4996083
|
||||
50 1.4999347 -0.87369019 0 1.3756625 1.4995685
|
||||
60 1.4998637 -0.87358381 0 1.3756625 1.4994975
|
||||
70 1.4997506 -0.87341428 0 1.3756624 1.4993845
|
||||
80 1.4995842 -0.87316464 0 1.3756624 1.499218
|
||||
90 1.4993536 -0.87281897 0 1.3756624 1.4989876
|
||||
100 1.4990503 -0.87236411 0 1.3756624 1.4986843
|
||||
Loop time of 2.73149 on 2 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 15815.560 tau/day, 36.610 timesteps/s
|
||||
99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00070763 | 0.00071537 | 0.00072312 | 0.0 | 0.03
|
||||
Kspace | 2.7111 | 2.7112 | 2.7112 | 0.0 | 99.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0096555 | 0.0097489 | 0.0098424 | 0.1 | 0.36
|
||||
Output | 0.00036025 | 0.0003823 | 0.00040436 | 0.0 | 0.01
|
||||
Modify | 0.0063472 | 0.0064594 | 0.0065715 | 0.1 | 0.24
|
||||
Other | | 0.00299 | | | 0.11
|
||||
|
||||
Nlocal: 2048 ave 2048 max 2048 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3685 ave 3685 max 3685 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 32768 ave 32768 max 32768 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000329494 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.497 | 3.497 | 3.497 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87378819 0 1.3756625 1.4996338
|
||||
10 1.5000004 -0.87378882 0 1.3756625 1.4996342
|
||||
20 1.4999998 -0.87378782 0 1.3756625 1.4996336
|
||||
30 1.4999934 -0.87377823 0 1.3756625 1.4996272
|
||||
40 1.4999745 -0.87374997 0 1.3756625 1.4996083
|
||||
50 1.4999347 -0.87369019 0 1.3756625 1.4995685
|
||||
60 1.4998637 -0.87358381 0 1.3756625 1.4994975
|
||||
70 1.4997506 -0.87341428 0 1.3756624 1.4993845
|
||||
80 1.4995842 -0.87316464 0 1.3756624 1.499218
|
||||
90 1.4993536 -0.87281897 0 1.3756624 1.4989876
|
||||
100 1.4990503 -0.87236411 0 1.3756624 1.4986843
|
||||
Loop time of 1.53742 on 4 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 28099.005 tau/day, 65.044 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00044894 | 0.00045562 | 0.0004611 | 0.0 | 0.03
|
||||
Kspace | 1.5223 | 1.5225 | 1.5225 | 0.0 | 99.03
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0085156 | 0.0086777 | 0.0088782 | 0.1 | 0.56
|
||||
Output | 0.00034738 | 0.0003686 | 0.0004015 | 0.0 | 0.02
|
||||
Modify | 0.0032606 | 0.0033693 | 0.0034289 | 0.1 | 0.22
|
||||
Other | | 0.002084 | | | 0.14
|
||||
|
||||
Nlocal: 1024 ave 1024 max 1024 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2525 ave 2525 max 2525 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 16384 ave 16384 max 16384 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000284672 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.416 | 3.416 | 3.416 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87378819 0 1.3756625 1.4996338
|
||||
10 1.5000004 -0.87378882 0 1.3756625 1.4996342
|
||||
20 1.4999998 -0.87378782 0 1.3756625 1.4996336
|
||||
30 1.4999934 -0.87377823 0 1.3756625 1.4996272
|
||||
40 1.4999745 -0.87374997 0 1.3756625 1.4996083
|
||||
50 1.4999347 -0.87369019 0 1.3756625 1.4995685
|
||||
60 1.4998637 -0.87358381 0 1.3756625 1.4994975
|
||||
70 1.4997506 -0.87341428 0 1.3756624 1.4993845
|
||||
80 1.4995842 -0.87316464 0 1.3756624 1.499218
|
||||
90 1.4993536 -0.87281897 0 1.3756624 1.4989876
|
||||
100 1.4990503 -0.87236411 0 1.3756624 1.4986843
|
||||
Loop time of 0.902102 on 8 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 47888.152 tau/day, 110.852 timesteps/s
|
||||
99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00030732 | 0.00031349 | 0.00032663 | 0.0 | 0.03
|
||||
Kspace | 0.89112 | 0.89138 | 0.8916 | 0.0 | 98.81
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0064399 | 0.0066807 | 0.0070164 | 0.2 | 0.74
|
||||
Output | 0.00034571 | 0.00036666 | 0.00041723 | 0.0 | 0.04
|
||||
Modify | 0.0018673 | 0.0019273 | 0.0020192 | 0.1 | 0.21
|
||||
Other | | 0.001431 | | | 0.16
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1685 ave 1685 max 1685 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8192 ave 8192 max 8192 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000631332 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.723 | 3.723 | 3.723 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87394226 0 1.3755084 1.4996338
|
||||
10 1.5000144 -0.87365638 0 1.375816 1.4996482
|
||||
20 1.5000284 -0.87366526 0 1.3758281 1.4996622
|
||||
30 1.5000364 -0.87366516 0 1.3758401 1.4996702
|
||||
40 1.5000313 -0.8736496 0 1.375848 1.4996651
|
||||
50 1.5000039 -0.87360069 0 1.3758558 1.4996377
|
||||
60 1.4999432 -0.87350118 0 1.3758644 1.499577
|
||||
70 1.499838 -0.87333517 0 1.3758726 1.4994719
|
||||
80 1.4996772 -0.87308644 0 1.3758801 1.4993111
|
||||
90 1.4994505 -0.87274307 0 1.3758836 1.4990844
|
||||
100 1.4991498 -0.8722911 0 1.3758846 1.4987838
|
||||
Loop time of 9.59682 on 1 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 4501.489 tau/day, 10.420 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0011375 | 0.0011375 | 0.0011375 | 0.0 | 0.01
|
||||
Kspace | 9.5688 | 9.5688 | 9.5688 | 0.0 | 99.71
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.009017 | 0.009017 | 0.009017 | 0.0 | 0.09
|
||||
Output | 0.0004344 | 0.0004344 | 0.0004344 | 0.0 | 0.00
|
||||
Modify | 0.012987 | 0.012987 | 0.012987 | 0.0 | 0.14
|
||||
Other | | 0.004481 | | | 0.05
|
||||
|
||||
Nlocal: 4096 ave 4096 max 4096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5165 ave 5165 max 5165 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 65536 ave 65536 max 65536 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:10
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
2 by 2 by 4 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000500917 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.401 | 3.401 | 3.401 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87394226 0 1.3755084 1.4996338
|
||||
10 1.5000144 -0.87365638 0 1.375816 1.4996482
|
||||
20 1.5000284 -0.87366526 0 1.3758281 1.4996622
|
||||
30 1.5000364 -0.87366516 0 1.3758401 1.4996702
|
||||
40 1.5000313 -0.8736496 0 1.375848 1.4996651
|
||||
50 1.5000039 -0.87360069 0 1.3758558 1.4996377
|
||||
60 1.4999432 -0.87350118 0 1.3758644 1.499577
|
||||
70 1.499838 -0.87333517 0 1.3758726 1.4994719
|
||||
80 1.4996772 -0.87308644 0 1.3758801 1.4993111
|
||||
90 1.4994505 -0.87274307 0 1.3758836 1.4990844
|
||||
100 1.4991498 -0.8722911 0 1.3758846 1.4987838
|
||||
Loop time of 1.20528 on 16 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 35842.175 tau/day, 82.968 timesteps/s
|
||||
99.3% CPU use with 16 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00021839 | 0.00025332 | 0.00029278 | 0.0 | 0.02
|
||||
Kspace | 1.1945 | 1.1948 | 1.195 | 0.0 | 99.13
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0066545 | 0.0069329 | 0.0072389 | 0.2 | 0.58
|
||||
Output | 0.0003922 | 0.00042732 | 0.00054955 | 0.0 | 0.04
|
||||
Modify | 0.0010166 | 0.0011965 | 0.0014412 | 0.3 | 0.10
|
||||
Other | | 0.001724 | | | 0.14
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1265 ave 1265 max 1265 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4096 ave 4096 max 4096 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.00044775 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.634 | 3.634 | 3.634 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87394226 0 1.3755084 1.4996338
|
||||
10 1.5000144 -0.87365638 0 1.375816 1.4996482
|
||||
20 1.5000284 -0.87366526 0 1.3758281 1.4996622
|
||||
30 1.5000364 -0.87366516 0 1.3758401 1.4996702
|
||||
40 1.5000313 -0.8736496 0 1.375848 1.4996651
|
||||
50 1.5000039 -0.87360069 0 1.3758558 1.4996377
|
||||
60 1.4999432 -0.87350118 0 1.3758644 1.499577
|
||||
70 1.499838 -0.87333517 0 1.3758726 1.4994719
|
||||
80 1.4996772 -0.87308644 0 1.3758801 1.4993111
|
||||
90 1.4994505 -0.87274307 0 1.3758836 1.4990844
|
||||
100 1.4991498 -0.8722911 0 1.3758846 1.4987838
|
||||
Loop time of 5.14681 on 2 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 8393.542 tau/day, 19.429 timesteps/s
|
||||
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00070882 | 0.00072873 | 0.00074863 | 0.0 | 0.01
|
||||
Kspace | 5.1257 | 5.1258 | 5.1258 | 0.0 | 99.59
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.010188 | 0.010291 | 0.010394 | 0.1 | 0.20
|
||||
Output | 0.00042391 | 0.00044322 | 0.00046253 | 0.0 | 0.01
|
||||
Modify | 0.0063772 | 0.006551 | 0.0067248 | 0.2 | 0.13
|
||||
Other | | 0.003026 | | | 0.06
|
||||
|
||||
Nlocal: 2048 ave 2048 max 2048 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3685 ave 3685 max 3685 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 32768 ave 32768 max 32768 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000317335 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.497 | 3.497 | 3.497 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87394226 0 1.3755084 1.4996338
|
||||
10 1.5000144 -0.87365638 0 1.375816 1.4996482
|
||||
20 1.5000284 -0.87366526 0 1.3758281 1.4996622
|
||||
30 1.5000364 -0.87366516 0 1.3758401 1.4996702
|
||||
40 1.5000313 -0.8736496 0 1.375848 1.4996651
|
||||
50 1.5000039 -0.87360069 0 1.3758558 1.4996377
|
||||
60 1.4999432 -0.87350118 0 1.3758644 1.499577
|
||||
70 1.499838 -0.87333517 0 1.3758726 1.4994719
|
||||
80 1.4996772 -0.87308644 0 1.3758801 1.4993111
|
||||
90 1.4994505 -0.87274307 0 1.3758836 1.4990844
|
||||
100 1.4991498 -0.8722911 0 1.3758846 1.4987838
|
||||
Loop time of 2.94274 on 4 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 14680.187 tau/day, 33.982 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00048852 | 0.00049287 | 0.00050163 | 0.0 | 0.02
|
||||
Kspace | 2.9277 | 2.9279 | 2.928 | 0.0 | 99.49
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0081494 | 0.0083126 | 0.0084655 | 0.1 | 0.28
|
||||
Output | 0.00034475 | 0.00040233 | 0.00043464 | 0.0 | 0.01
|
||||
Modify | 0.0034239 | 0.0035145 | 0.0036252 | 0.1 | 0.12
|
||||
Other | | 0.00216 | | | 0.07
|
||||
|
||||
Nlocal: 1024 ave 1024 max 1024 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2525 ave 2525 max 2525 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 16384 ave 16384 max 16384 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8
Normal file
102
examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaCl
|
||||
orthogonal box = (0 0 0) to (2 2 2)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
|
||||
replicate 8 8 8
|
||||
orthogonal box = (0 0 0) to (16 16 16)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
4096 atoms
|
||||
Time spent = 0.000422239 secs
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance field
|
||||
|
||||
timestep 0.005
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.416 | 3.416 | 3.416 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.87394226 0 1.3755084 1.4996338
|
||||
10 1.5000144 -0.87365638 0 1.375816 1.4996482
|
||||
20 1.5000284 -0.87366526 0 1.3758281 1.4996622
|
||||
30 1.5000364 -0.87366516 0 1.3758401 1.4996702
|
||||
40 1.5000313 -0.8736496 0 1.375848 1.4996651
|
||||
50 1.5000039 -0.87360069 0 1.3758558 1.4996377
|
||||
60 1.4999432 -0.87350118 0 1.3758644 1.499577
|
||||
70 1.499838 -0.87333517 0 1.3758726 1.4994719
|
||||
80 1.4996772 -0.87308644 0 1.3758801 1.4993111
|
||||
90 1.4994505 -0.87274307 0 1.3758836 1.4990844
|
||||
100 1.4991498 -0.8722911 0 1.3758846 1.4987838
|
||||
Loop time of 1.75933 on 8 procs for 100 steps with 4096 atoms
|
||||
|
||||
Performance: 24554.819 tau/day, 56.840 timesteps/s
|
||||
99.4% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00030684 | 0.00031838 | 0.00032926 | 0.0 | 0.02
|
||||
Kspace | 1.7474 | 1.7477 | 1.748 | 0.0 | 99.34
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0068667 | 0.0072413 | 0.0075011 | 0.2 | 0.41
|
||||
Output | 0.00036955 | 0.00038695 | 0.00044942 | 0.0 | 0.02
|
||||
Modify | 0.0018206 | 0.0019438 | 0.0020213 | 0.1 | 0.11
|
||||
Other | | 0.001739 | | | 0.10
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1685 ave 1685 max 1685 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8192 ave 8192 max 8192 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 65536
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
105
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1
Normal file
105
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos direct 0.001
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver direct ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 10.3 | 10.3 | 10.3 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417787 0 1.6235721 0.00141207
|
||||
1 18.780041 -10.770002 0 17.371889 0.017679155
|
||||
2 65.289192 -11.084705 0 86.751149 0.06146194
|
||||
3 121.92987 -7.0625759 0 175.64933 0.11478234
|
||||
4 185.78164 -5.8777512 0 272.51604 0.17489112
|
||||
5 286.36222 -4.382053 0 424.73173 0.26957567
|
||||
6 481.42206 -4.3095567 0 717.1014 0.4532011
|
||||
7 488.59167 -3.8685194 0 728.2861 0.45995044
|
||||
8 497.85287 -3.0417966 0 742.99073 0.46866874
|
||||
9 499.61615 -3.419003 0 745.2558 0.47032866
|
||||
10 502.63684 -2.8360961 0 750.36521 0.47317227
|
||||
11 504.4846 -2.7628105 0 753.20736 0.47491172
|
||||
12 506.54485 -2.8460356 0 756.21142 0.47685119
|
||||
13 508.27211 -2.730935 0 758.91482 0.4784772
|
||||
14 510.57045 -2.6094877 0 762.48033 0.48064081
|
||||
15 513.14798 -2.7150827 0 766.23717 0.48306726
|
||||
16 515.78124 -2.3961811 0 770.50201 0.48554615
|
||||
17 515.70265 -2.2982683 0 770.48215 0.48547216
|
||||
18 515.7081 -2.1515983 0 770.63699 0.4854773
|
||||
19 515.74906 -2.0581436 0 770.79182 0.48551586
|
||||
20 515.70883 -1.8922577 0 770.89742 0.48547798
|
||||
Loop time of 0.52055 on 1 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 16597.836 tau/day, 38.421 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05
|
||||
Kspace | 0.35879 | 0.35879 | 0.35879 | 0.0 | 68.93
|
||||
Neigh | 0.15946 | 0.15946 | 0.15946 | 0.0 | 30.63
|
||||
Comm | 0.00024056 | 0.00024056 | 0.00024056 | 0.0 | 0.05
|
||||
Output | 0.00034761 | 0.00034761 | 0.00034761 | 0.0 | 0.07
|
||||
Modify | 0.00071192 | 0.00071192 | 0.00071192 | 0.0 | 0.14
|
||||
Other | | 0.0007269 | | | 0.14
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 247817 ave 247817 max 247817 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 247817
|
||||
Ave neighs/atom = 247.817
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:00
|
||||
105
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2
Normal file
105
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos direct 0.001
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver direct ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 6.48 | 6.861 | 7.243 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417787 0 1.6235721 0.00141207
|
||||
1 18.780041 -10.770002 0 17.371889 0.017679155
|
||||
2 65.289192 -11.084705 0 86.751149 0.06146194
|
||||
3 121.92987 -7.0625759 0 175.64933 0.11478234
|
||||
4 185.78164 -5.8777512 0 272.51604 0.17489112
|
||||
5 286.36222 -4.382053 0 424.73173 0.26957567
|
||||
6 481.42206 -4.3095567 0 717.1014 0.4532011
|
||||
7 488.59167 -3.8685194 0 728.2861 0.45995044
|
||||
8 497.85287 -3.0417966 0 742.99073 0.46866874
|
||||
9 499.61615 -3.419003 0 745.2558 0.47032866
|
||||
10 502.63684 -2.8360961 0 750.36521 0.47317227
|
||||
11 504.4846 -2.7628105 0 753.20736 0.47491172
|
||||
12 506.54485 -2.8460356 0 756.21142 0.47685119
|
||||
13 508.27211 -2.730935 0 758.91482 0.4784772
|
||||
14 510.57045 -2.6094877 0 762.48033 0.48064081
|
||||
15 513.14798 -2.7150827 0 766.23717 0.48306726
|
||||
16 515.78124 -2.3961811 0 770.50201 0.48554615
|
||||
17 515.70265 -2.2982683 0 770.48215 0.48547216
|
||||
18 515.7081 -2.1515983 0 770.63699 0.4854773
|
||||
19 515.74906 -2.0581436 0 770.79182 0.48551586
|
||||
20 515.70883 -1.8922577 0 770.89742 0.48547798
|
||||
Loop time of 0.330519 on 2 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 26140.700 tau/day, 60.511 timesteps/s
|
||||
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0002749 | 0.00027692 | 0.00027895 | 0.0 | 0.08
|
||||
Kspace | 0.21565 | 0.24173 | 0.26782 | 5.3 | 73.14
|
||||
Neigh | 0.058644 | 0.084906 | 0.11117 | 9.0 | 25.69
|
||||
Comm | 0.002033 | 0.0022832 | 0.0025334 | 0.5 | 0.69
|
||||
Output | 0.00035667 | 0.0004549 | 0.00055313 | 0.0 | 0.14
|
||||
Modify | 0.0004704 | 0.00050521 | 0.00054002 | 0.0 | 0.15
|
||||
Other | | 0.0003613 | | | 0.11
|
||||
|
||||
Nlocal: 500 ave 516 max 484 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 456.5 ave 475 max 438 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 123908 ave 172139 max 75678 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 247817
|
||||
Ave neighs/atom = 247.817
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:00
|
||||
105
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4
Normal file
105
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos direct 0.001
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver direct ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 4.837 | 5.123 | 5.6 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417787 0 1.6235721 0.00141207
|
||||
1 18.780041 -10.770002 0 17.371889 0.017679155
|
||||
2 65.289192 -11.084705 0 86.751149 0.06146194
|
||||
3 121.92987 -7.0625759 0 175.64933 0.11478234
|
||||
4 185.78164 -5.8777512 0 272.51604 0.17489112
|
||||
5 286.36222 -4.382053 0 424.73173 0.26957567
|
||||
6 481.42206 -4.3095567 0 717.1014 0.4532011
|
||||
7 488.59167 -3.8685194 0 728.2861 0.45995044
|
||||
8 497.85287 -3.0417966 0 742.99073 0.46866874
|
||||
9 499.61615 -3.419003 0 745.2558 0.47032866
|
||||
10 502.63684 -2.8360961 0 750.36521 0.47317227
|
||||
11 504.4846 -2.7628105 0 753.20736 0.47491172
|
||||
12 506.54485 -2.8460356 0 756.21142 0.47685119
|
||||
13 508.27211 -2.730935 0 758.91482 0.4784772
|
||||
14 510.57045 -2.6094877 0 762.48033 0.48064081
|
||||
15 513.14798 -2.7150827 0 766.23717 0.48306726
|
||||
16 515.78124 -2.3961811 0 770.50201 0.48554615
|
||||
17 515.70265 -2.2982683 0 770.48215 0.48547216
|
||||
18 515.7081 -2.1515983 0 770.63699 0.4854773
|
||||
19 515.74906 -2.0581436 0 770.79182 0.48551586
|
||||
20 515.70883 -1.8922577 0 770.89742 0.48547798
|
||||
Loop time of 0.197141 on 4 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 43826.435 tau/day, 101.450 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0002718 | 0.00027621 | 0.00028539 | 0.0 | 0.14
|
||||
Kspace | 0.12861 | 0.14654 | 0.16542 | 3.7 | 74.33
|
||||
Neigh | 0.027906 | 0.046895 | 0.064943 | 6.6 | 23.79
|
||||
Comm | 0.0022087 | 0.0024236 | 0.0026295 | 0.4 | 1.23
|
||||
Output | 0.0003252 | 0.00044608 | 0.0006001 | 0.0 | 0.23
|
||||
Modify | 0.00016618 | 0.0001756 | 0.00018811 | 0.0 | 0.09
|
||||
Other | | 0.0003839 | | | 0.19
|
||||
|
||||
Nlocal: 250 ave 259 max 238 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Nghost: 672.25 ave 683 max 663 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 61954.2 ave 97157 max 25016 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 247817
|
||||
Ave neighs/atom = 247.817
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:00
|
||||
105
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8
Normal file
105
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos direct 0.001
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver direct ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 4.164 | 4.26 | 4.546 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417787 0 1.6235721 0.00141207
|
||||
1 18.780041 -10.770002 0 17.371889 0.017679155
|
||||
2 65.289192 -11.084705 0 86.751149 0.06146194
|
||||
3 121.92987 -7.0625759 0 175.64933 0.11478234
|
||||
4 185.78164 -5.8777512 0 272.51604 0.17489112
|
||||
5 286.36222 -4.382053 0 424.73173 0.26957567
|
||||
6 481.42206 -4.3095567 0 717.1014 0.4532011
|
||||
7 488.59167 -3.8685194 0 728.2861 0.45995044
|
||||
8 497.85287 -3.0417966 0 742.99073 0.46866874
|
||||
9 499.61615 -3.419003 0 745.2558 0.47032866
|
||||
10 502.63684 -2.8360961 0 750.36521 0.47317227
|
||||
11 504.4846 -2.7628105 0 753.20736 0.47491172
|
||||
12 506.54485 -2.8460356 0 756.21142 0.47685119
|
||||
13 508.27211 -2.730935 0 758.91482 0.4784772
|
||||
14 510.57045 -2.6094877 0 762.48033 0.48064081
|
||||
15 513.14798 -2.7150827 0 766.23717 0.48306726
|
||||
16 515.78124 -2.3961811 0 770.50201 0.48554615
|
||||
17 515.70265 -2.2982683 0 770.48215 0.48547216
|
||||
18 515.7081 -2.1515983 0 770.63699 0.4854773
|
||||
19 515.74906 -2.0581436 0 770.79182 0.48551586
|
||||
20 515.70883 -1.8922577 0 770.89742 0.48547798
|
||||
Loop time of 0.107014 on 8 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 80736.875 tau/day, 186.891 timesteps/s
|
||||
98.8% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027704 | 0.00029281 | 0.00035691 | 0.0 | 0.27
|
||||
Kspace | 0.069458 | 0.07877 | 0.089146 | 2.5 | 73.61
|
||||
Neigh | 0.013525 | 0.024156 | 0.033524 | 4.7 | 22.57
|
||||
Comm | 0.002552 | 0.0029828 | 0.0033691 | 0.5 | 2.79
|
||||
Output | 0.00037909 | 0.00051123 | 0.00070429 | 0.0 | 0.48
|
||||
Modify | 8.9645e-05 | 9.5487e-05 | 0.000103 | 0.0 | 0.09
|
||||
Other | | 0.0002059 | | | 0.19
|
||||
|
||||
Nlocal: 125 ave 133 max 113 min
|
||||
Histogram: 2 0 0 0 0 1 1 0 2 2
|
||||
Nghost: 773.625 ave 788 max 764 min
|
||||
Histogram: 1 1 2 1 1 0 0 0 1 1
|
||||
Neighs: 30977.1 ave 50690 max 10447 min
|
||||
Histogram: 1 1 1 0 1 1 0 0 2 1
|
||||
|
||||
Total # of neighbors = 247817
|
||||
Ave neighs/atom = 247.817
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:00
|
||||
109
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1
Normal file
109
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1
Normal file
@ -0,0 +1,109 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 10.3 | 10.3 | 10.3 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417141 0 1.6235786 0.00141207
|
||||
1 18.780412 -10.770009 0 17.372438 0.017679504
|
||||
2 65.294131 -11.084501 0 86.758754 0.06146659
|
||||
3 121.92555 -7.0612033 0 175.64423 0.11477827
|
||||
4 185.71165 -5.8781334 0 272.41077 0.17482523
|
||||
5 286.28339 -4.3800108 0 424.61565 0.26950146
|
||||
6 481.28097 -4.3052012 0 716.89433 0.45306828
|
||||
7 487.26022 -3.8672741 0 726.29216 0.45869703
|
||||
8 493.65478 -3.0242687 0 736.71742 0.46471675
|
||||
9 495.66203 -3.4336343 0 739.31592 0.46660633
|
||||
10 498.41831 -2.8837072 0 743.99613 0.46920104
|
||||
11 499.20944 -2.7724783 0 745.29287 0.46994579
|
||||
12 500.97345 -2.8281484 0 747.88057 0.4716064
|
||||
13 507.46412 -2.7752775 0 757.65971 0.47771658
|
||||
14 525.35729 -2.5749814 0 784.67292 0.49456085
|
||||
15 563.9578 -2.9982381 0 842.09253 0.5308986
|
||||
16 645.47602 -2.5519203 0 964.69389 0.60763822
|
||||
17 647.09276 -2.2568468 0 967.41166 0.60916019
|
||||
18 647.12596 -2.2791003 0 967.43915 0.60919144
|
||||
19 647.24862 -2.2495226 0 967.65253 0.60930691
|
||||
20 647.51175 -2.0239179 0 968.27244 0.60955462
|
||||
Loop time of 0.644143 on 1 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 13413.173 tau/day, 31.049 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027657 | 0.00027657 | 0.00027657 | 0.0 | 0.04
|
||||
Kspace | 0.4788 | 0.4788 | 0.4788 | 0.0 | 74.33
|
||||
Neigh | 0.16279 | 0.16279 | 0.16279 | 0.0 | 25.27
|
||||
Comm | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.03
|
||||
Output | 0.00054836 | 0.00054836 | 0.00054836 | 0.0 | 0.09
|
||||
Modify | 0.00075102 | 0.00075102 | 0.00075102 | 0.0 | 0.12
|
||||
Other | | 0.000757 | | | 0.12
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 244342 ave 244342 max 244342 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 244342
|
||||
Ave neighs/atom = 244.342
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:00
|
||||
109
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2
Normal file
109
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2
Normal file
@ -0,0 +1,109 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 6.48 | 6.861 | 7.243 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417141 0 1.6235786 0.00141207
|
||||
1 18.780412 -10.770009 0 17.372438 0.017679504
|
||||
2 65.294131 -11.084501 0 86.758754 0.06146659
|
||||
3 121.92555 -7.0612033 0 175.64423 0.11477827
|
||||
4 185.71165 -5.8781334 0 272.41077 0.17482523
|
||||
5 286.28339 -4.3800108 0 424.61565 0.26950146
|
||||
6 481.28097 -4.3052012 0 716.89433 0.45306828
|
||||
7 487.26022 -3.8672741 0 726.29216 0.45869703
|
||||
8 493.65478 -3.0242687 0 736.71742 0.46471675
|
||||
9 495.66203 -3.4336343 0 739.31592 0.46660633
|
||||
10 498.41831 -2.8837072 0 743.99613 0.46920104
|
||||
11 499.20944 -2.7724783 0 745.29287 0.46994579
|
||||
12 500.97345 -2.8281484 0 747.88057 0.4716064
|
||||
13 507.46412 -2.7752775 0 757.65971 0.47771658
|
||||
14 525.35729 -2.5749814 0 784.67292 0.49456085
|
||||
15 563.9578 -2.9982381 0 842.09253 0.5308986
|
||||
16 645.47602 -2.5519203 0 964.69389 0.60763822
|
||||
17 647.09276 -2.2568468 0 967.41166 0.60916019
|
||||
18 647.12596 -2.2791003 0 967.43915 0.60919144
|
||||
19 647.24862 -2.2495226 0 967.65253 0.60930691
|
||||
20 647.51175 -2.0239179 0 968.27244 0.60955462
|
||||
Loop time of 0.563049 on 2 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 15345.024 tau/day, 35.521 timesteps/s
|
||||
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00024986 | 0.00026596 | 0.00028205 | 0.0 | 0.05
|
||||
Kspace | 0.45103 | 0.47692 | 0.50281 | 3.7 | 84.70
|
||||
Neigh | 0.055771 | 0.081813 | 0.10785 | 9.1 | 14.53
|
||||
Comm | 0.0022206 | 0.0024507 | 0.0026808 | 0.5 | 0.44
|
||||
Output | 0.00050044 | 0.00061882 | 0.00073719 | 0.0 | 0.11
|
||||
Modify | 0.00029945 | 0.00044227 | 0.00058508 | 0.0 | 0.08
|
||||
Other | | 0.0005381 | | | 0.10
|
||||
|
||||
Nlocal: 500 ave 509 max 491 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 455.5 ave 467 max 444 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 122171 ave 171834 max 72508 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 244342
|
||||
Ave neighs/atom = 244.342
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:01
|
||||
109
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4
Normal file
109
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4
Normal file
@ -0,0 +1,109 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 4.837 | 5.123 | 5.6 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417141 0 1.6235786 0.00141207
|
||||
1 18.780412 -10.770009 0 17.372438 0.017679504
|
||||
2 65.294131 -11.084501 0 86.758754 0.06146659
|
||||
3 121.92555 -7.0612033 0 175.64423 0.11477827
|
||||
4 185.71165 -5.8781334 0 272.41077 0.17482523
|
||||
5 286.28339 -4.3800108 0 424.61565 0.26950146
|
||||
6 481.28097 -4.3052012 0 716.89433 0.45306828
|
||||
7 487.26022 -3.8672741 0 726.29216 0.45869703
|
||||
8 493.65478 -3.0242687 0 736.71742 0.46471675
|
||||
9 495.66203 -3.4336343 0 739.31592 0.46660633
|
||||
10 498.41831 -2.8837072 0 743.99613 0.46920104
|
||||
11 499.20944 -2.7724783 0 745.29287 0.46994579
|
||||
12 500.97345 -2.8281484 0 747.88057 0.4716064
|
||||
13 507.46412 -2.7752775 0 757.65971 0.47771658
|
||||
14 525.35729 -2.5749814 0 784.67292 0.49456085
|
||||
15 563.9578 -2.9982381 0 842.09253 0.5308986
|
||||
16 645.47602 -2.5519203 0 964.69389 0.60763822
|
||||
17 647.09276 -2.2568468 0 967.41166 0.60916019
|
||||
18 647.12596 -2.2791003 0 967.43915 0.60919144
|
||||
19 647.24862 -2.2495226 0 967.65253 0.60930691
|
||||
20 647.51175 -2.0239179 0 968.27244 0.60955462
|
||||
Loop time of 0.508149 on 4 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 17002.884 tau/day, 39.359 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00024509 | 0.00026453 | 0.00028753 | 0.0 | 0.05
|
||||
Kspace | 0.43933 | 0.45836 | 0.47734 | 2.2 | 90.20
|
||||
Neigh | 0.025956 | 0.045068 | 0.064242 | 7.2 | 8.87
|
||||
Comm | 0.002799 | 0.0030612 | 0.0033174 | 0.4 | 0.60
|
||||
Output | 0.00047231 | 0.00058293 | 0.00076509 | 0.0 | 0.11
|
||||
Modify | 0.00016856 | 0.0002442 | 0.00042009 | 0.0 | 0.05
|
||||
Other | | 0.0005655 | | | 0.11
|
||||
|
||||
Nlocal: 250 ave 259 max 240 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 668.75 ave 679 max 657 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 61085.5 ave 95363 max 24964 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 244342
|
||||
Ave neighs/atom = 244.342
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:01
|
||||
109
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8
Normal file
109
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8
Normal file
@ -0,0 +1,109 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos fmm 0.001
|
||||
kspace_modify scafacos tolerance energy_rel
|
||||
kspace_modify scafacos fmm_tuning 1
|
||||
ScaFaCoS setting fmm inhomogen tuning ...3
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver fmm ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 4.164 | 4.26 | 4.546 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417141 0 1.6235786 0.00141207
|
||||
1 18.780412 -10.770009 0 17.372438 0.017679504
|
||||
2 65.294131 -11.084501 0 86.758754 0.06146659
|
||||
3 121.92555 -7.0612033 0 175.64423 0.11477827
|
||||
4 185.71165 -5.8781334 0 272.41077 0.17482523
|
||||
5 286.28339 -4.3800108 0 424.61565 0.26950146
|
||||
6 481.28097 -4.3052012 0 716.89433 0.45306828
|
||||
7 487.26022 -3.8672741 0 726.29216 0.45869703
|
||||
8 493.65478 -3.0242687 0 736.71742 0.46471675
|
||||
9 495.66203 -3.4336343 0 739.31592 0.46660633
|
||||
10 498.41831 -2.8837072 0 743.99613 0.46920104
|
||||
11 499.20944 -2.7724783 0 745.29287 0.46994579
|
||||
12 500.97345 -2.8281484 0 747.88057 0.4716064
|
||||
13 507.46412 -2.7752775 0 757.65971 0.47771658
|
||||
14 525.35729 -2.5749814 0 784.67292 0.49456085
|
||||
15 563.9578 -2.9982381 0 842.09253 0.5308986
|
||||
16 645.47602 -2.5519203 0 964.69389 0.60763822
|
||||
17 647.09276 -2.2568468 0 967.41166 0.60916019
|
||||
18 647.12596 -2.2791003 0 967.43915 0.60919144
|
||||
19 647.24862 -2.2495226 0 967.65253 0.60930691
|
||||
20 647.51175 -2.0239179 0 968.27244 0.60955462
|
||||
Loop time of 0.494261 on 8 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 17480.630 tau/day, 40.464 timesteps/s
|
||||
99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027752 | 0.00030088 | 0.0003736 | 0.0 | 0.06
|
||||
Kspace | 0.45443 | 0.46295 | 0.47316 | 1.0 | 93.67
|
||||
Neigh | 0.014408 | 0.02515 | 0.034048 | 4.6 | 5.09
|
||||
Comm | 0.0036254 | 0.0041741 | 0.0048032 | 0.6 | 0.84
|
||||
Output | 0.00072742 | 0.0009357 | 0.0012984 | 0.0 | 0.19
|
||||
Modify | 0.00011778 | 0.00015756 | 0.00019836 | 0.0 | 0.03
|
||||
Other | | 0.000589 | | | 0.12
|
||||
|
||||
Nlocal: 125 ave 137 max 111 min
|
||||
Histogram: 1 1 0 0 0 2 2 1 0 1
|
||||
Nghost: 768.875 ave 788 max 761 min
|
||||
Histogram: 4 0 2 0 0 0 1 0 0 1
|
||||
Neighs: 30542.8 ave 48077 max 10011 min
|
||||
Histogram: 1 1 1 0 1 1 0 0 0 3
|
||||
|
||||
Total # of neighbors = 244342
|
||||
Ave neighs/atom = 244.342
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:01
|
||||
107
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1
Normal file
107
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1
Normal file
@ -0,0 +1,107 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance potential
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 10.3 | 10.3 | 10.3 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417787 0 1.6235721 0.00141207
|
||||
1 18.780041 -10.770002 0 17.371889 0.017679155
|
||||
2 65.289192 -11.084705 0 86.751149 0.06146194
|
||||
3 121.92987 -7.0625759 0 175.64933 0.11478234
|
||||
4 185.78164 -5.8777511 0 272.51603 0.17489112
|
||||
5 286.36221 -4.3820531 0 424.73172 0.26957566
|
||||
6 481.42203 -4.3095567 0 717.10136 0.45320108
|
||||
7 488.59165 -3.8685193 0 728.28607 0.45995042
|
||||
8 497.85288 -3.0417938 0 742.99075 0.46866875
|
||||
9 499.61619 -3.4190063 0 745.25585 0.47032869
|
||||
10 502.63691 -2.8360951 0 750.36531 0.47317234
|
||||
11 504.4847 -2.7628089 0 753.20751 0.47491181
|
||||
12 506.54494 -2.8460319 0 756.21157 0.47685128
|
||||
13 508.2722 -2.7309328 0 758.91497 0.47847729
|
||||
14 510.57053 -2.6094792 0 762.48045 0.48064089
|
||||
15 513.14804 -2.7150819 0 766.23726 0.48306731
|
||||
16 515.78127 -2.3961749 0 770.50206 0.48554618
|
||||
17 515.70267 -2.2982581 0 770.48219 0.48547219
|
||||
18 515.70813 -2.1516075 0 770.63702 0.48547732
|
||||
19 515.74908 -2.0581483 0 770.79185 0.48551588
|
||||
20 515.70881 -1.892235 0 770.89742 0.48547797
|
||||
Loop time of 1.34132 on 1 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 6441.409 tau/day, 14.911 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00028849 | 0.00028849 | 0.00028849 | 0.0 | 0.02
|
||||
Kspace | 1.1744 | 1.1744 | 1.1744 | 0.0 | 87.56
|
||||
Neigh | 0.16435 | 0.16435 | 0.16435 | 0.0 | 12.25
|
||||
Comm | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02
|
||||
Output | 0.00051928 | 0.00051928 | 0.00051928 | 0.0 | 0.04
|
||||
Modify | 0.00079513 | 0.00079513 | 0.00079513 | 0.0 | 0.06
|
||||
Other | | 0.0007439 | | | 0.06
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 247817 ave 247817 max 247817 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 247817
|
||||
Ave neighs/atom = 247.817
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:01
|
||||
107
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2
Normal file
107
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2
Normal file
@ -0,0 +1,107 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance potential
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 6.48 | 6.861 | 7.243 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417787 0 1.6235721 0.00141207
|
||||
1 18.780041 -10.770002 0 17.371889 0.017679155
|
||||
2 65.289192 -11.084705 0 86.751149 0.06146194
|
||||
3 121.92987 -7.0625759 0 175.64933 0.11478234
|
||||
4 185.78164 -5.8777511 0 272.51603 0.17489112
|
||||
5 286.36221 -4.3820531 0 424.73172 0.26957566
|
||||
6 481.42203 -4.3095567 0 717.10136 0.45320108
|
||||
7 488.59165 -3.8685193 0 728.28607 0.45995042
|
||||
8 497.85288 -3.0417938 0 742.99075 0.46866875
|
||||
9 499.61619 -3.4190063 0 745.25585 0.47032869
|
||||
10 502.63691 -2.8360951 0 750.36531 0.47317234
|
||||
11 504.4847 -2.7628089 0 753.20751 0.47491181
|
||||
12 506.54494 -2.8460319 0 756.21157 0.47685128
|
||||
13 508.2722 -2.7309328 0 758.91497 0.47847729
|
||||
14 510.57053 -2.6094792 0 762.48045 0.48064089
|
||||
15 513.14804 -2.7150819 0 766.23726 0.48306731
|
||||
16 515.78127 -2.3961749 0 770.50206 0.48554618
|
||||
17 515.70267 -2.2982581 0 770.48219 0.48547219
|
||||
18 515.70813 -2.1516075 0 770.63702 0.48547732
|
||||
19 515.74908 -2.0581483 0 770.79185 0.48551588
|
||||
20 515.70881 -1.892235 0 770.89742 0.48547797
|
||||
Loop time of 0.858675 on 2 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 10062.016 tau/day, 23.292 timesteps/s
|
||||
100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00026321 | 0.00026667 | 0.00027013 | 0.0 | 0.03
|
||||
Kspace | 0.74531 | 0.77182 | 0.79833 | 3.0 | 89.89
|
||||
Neigh | 0.055915 | 0.082578 | 0.10924 | 9.3 | 9.62
|
||||
Comm | 0.0021703 | 0.002401 | 0.0026317 | 0.5 | 0.28
|
||||
Output | 0.00048423 | 0.00061262 | 0.000741 | 0.0 | 0.07
|
||||
Modify | 0.00034285 | 0.0004636 | 0.00058436 | 0.0 | 0.05
|
||||
Other | | 0.0005329 | | | 0.06
|
||||
|
||||
Nlocal: 500 ave 516 max 484 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 456.5 ave 475 max 438 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 123908 ave 172139 max 75678 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 247817
|
||||
Ave neighs/atom = 247.817
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:01
|
||||
107
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4
Normal file
107
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4
Normal file
@ -0,0 +1,107 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance potential
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 4.837 | 5.123 | 5.6 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417787 0 1.6235721 0.00141207
|
||||
1 18.780041 -10.770002 0 17.371889 0.017679155
|
||||
2 65.289192 -11.084705 0 86.751149 0.06146194
|
||||
3 121.92987 -7.0625759 0 175.64933 0.11478234
|
||||
4 185.78164 -5.8777511 0 272.51603 0.17489112
|
||||
5 286.36221 -4.3820531 0 424.73172 0.26957566
|
||||
6 481.42203 -4.3095567 0 717.10136 0.45320108
|
||||
7 488.59165 -3.8685193 0 728.28607 0.45995042
|
||||
8 497.85288 -3.0417938 0 742.99075 0.46866875
|
||||
9 499.61619 -3.4190063 0 745.25585 0.47032869
|
||||
10 502.63691 -2.8360951 0 750.36531 0.47317234
|
||||
11 504.4847 -2.7628089 0 753.20751 0.47491181
|
||||
12 506.54494 -2.8460319 0 756.21157 0.47685128
|
||||
13 508.2722 -2.7309328 0 758.91497 0.47847729
|
||||
14 510.57053 -2.6094792 0 762.48045 0.48064089
|
||||
15 513.14804 -2.7150819 0 766.23726 0.48306731
|
||||
16 515.78127 -2.3961749 0 770.50206 0.48554618
|
||||
17 515.70267 -2.2982581 0 770.48219 0.48547219
|
||||
18 515.70813 -2.1516075 0 770.63702 0.48547732
|
||||
19 515.74908 -2.0581483 0 770.79185 0.48551588
|
||||
20 515.70881 -1.892235 0 770.89742 0.48547797
|
||||
Loop time of 0.540235 on 4 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 15993.051 tau/day, 37.021 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00025725 | 0.00028253 | 0.00031233 | 0.0 | 0.05
|
||||
Kspace | 0.47152 | 0.48989 | 0.50709 | 1.9 | 90.68
|
||||
Neigh | 0.028196 | 0.045694 | 0.064338 | 6.3 | 8.46
|
||||
Comm | 0.0026579 | 0.003028 | 0.0033965 | 0.5 | 0.56
|
||||
Output | 0.00049663 | 0.00064254 | 0.00084853 | 0.0 | 0.12
|
||||
Modify | 0.00019264 | 0.0002293 | 0.00030923 | 0.0 | 0.04
|
||||
Other | | 0.0004709 | | | 0.09
|
||||
|
||||
Nlocal: 250 ave 259 max 238 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Nghost: 672.25 ave 683 max 663 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 61954.2 ave 97157 max 25016 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 247817
|
||||
Ave neighs/atom = 247.817
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:00
|
||||
107
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8
Normal file
107
examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8
Normal file
@ -0,0 +1,107 @@
|
||||
LAMMPS (29 Jun 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
read_data data.hammersley_shphere
|
||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
change_box all boundary f f f
|
||||
|
||||
velocity all create 1.5 49893
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# LAMMPS computes pairwise and long-range Coulombics
|
||||
|
||||
#pair_style coul/long 3.0
|
||||
#pair_coeff * *
|
||||
#kspace_style pppm 1.0e-3
|
||||
|
||||
# Scafacos computes entire long-range Coulombics
|
||||
# use dummy pair style to perform atom sorting
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
#fix 2 all scafacos p3m tolerance field 0.001
|
||||
|
||||
kspace_style scafacos p2nfft 0.001
|
||||
kspace_modify scafacos tolerance potential
|
||||
|
||||
timestep 0.005
|
||||
thermo 1
|
||||
|
||||
run 20
|
||||
Setting up ScaFaCoS with solver p2nfft ...
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 102 102 102
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 4.164 | 4.26 | 4.546 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.5 -0.62417787 0 1.6235721 0.00141207
|
||||
1 18.780041 -10.770002 0 17.371889 0.017679155
|
||||
2 65.289192 -11.084705 0 86.751149 0.06146194
|
||||
3 121.92987 -7.0625759 0 175.64933 0.11478234
|
||||
4 185.78164 -5.8777511 0 272.51603 0.17489112
|
||||
5 286.36221 -4.3820531 0 424.73172 0.26957566
|
||||
6 481.42203 -4.3095567 0 717.10136 0.45320108
|
||||
7 488.59165 -3.8685193 0 728.28607 0.45995042
|
||||
8 497.85288 -3.0417938 0 742.99075 0.46866875
|
||||
9 499.61619 -3.4190063 0 745.25585 0.47032869
|
||||
10 502.63691 -2.8360951 0 750.36531 0.47317234
|
||||
11 504.4847 -2.7628089 0 753.20751 0.47491181
|
||||
12 506.54494 -2.8460319 0 756.21157 0.47685128
|
||||
13 508.2722 -2.7309328 0 758.91497 0.47847729
|
||||
14 510.57053 -2.6094792 0 762.48045 0.48064089
|
||||
15 513.14804 -2.7150819 0 766.23726 0.48306731
|
||||
16 515.78127 -2.3961749 0 770.50206 0.48554618
|
||||
17 515.70267 -2.2982581 0 770.48219 0.48547219
|
||||
18 515.70813 -2.1516075 0 770.63702 0.48547732
|
||||
19 515.74908 -2.0581483 0 770.79185 0.48551588
|
||||
20 515.70881 -1.892235 0 770.89742 0.48547797
|
||||
Loop time of 0.317433 on 8 procs for 20 steps with 1000 atoms
|
||||
|
||||
Performance: 27218.342 tau/day, 63.005 timesteps/s
|
||||
99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027013 | 0.00028479 | 0.00029206 | 0.0 | 0.09
|
||||
Kspace | 0.27742 | 0.28666 | 0.29702 | 1.4 | 90.31
|
||||
Neigh | 0.014795 | 0.025382 | 0.03481 | 4.8 | 8.00
|
||||
Comm | 0.0034907 | 0.0038758 | 0.0042439 | 0.5 | 1.22
|
||||
Output | 0.00055361 | 0.00073573 | 0.0010755 | 0.0 | 0.23
|
||||
Modify | 0.00012279 | 0.00014156 | 0.00016165 | 0.0 | 0.04
|
||||
Other | | 0.0003535 | | | 0.11
|
||||
|
||||
Nlocal: 125 ave 133 max 113 min
|
||||
Histogram: 2 0 0 0 0 1 1 0 2 2
|
||||
Nghost: 773.625 ave 788 max 764 min
|
||||
Histogram: 1 1 2 1 1 0 0 0 1 1
|
||||
Neighs: 30977.1 ave 50690 max 10447 min
|
||||
Histogram: 1 1 1 0 1 1 0 0 2 1
|
||||
|
||||
Total # of neighbors = 247817
|
||||
Ave neighs/atom = 247.817
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 18
|
||||
Total wall time: 0:00:00
|
||||
Reference in New Issue
Block a user