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Guillaume Fraux
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Create a framework for running and saving benchmarks
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‎.gitignore

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log.lammps

‎LAMMPS.in

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units real
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atom_style full
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boundary p p p
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read_data data/helium.lmp
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pair_style lj/cut 8
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pair_coeff 1 1 0.3 2.0
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neighbor 2.0 bin
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neigh_modify every 1 delay 0 check yes
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velocity all create 300.0 42 dist gaussian
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fix 1 all nve
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timestep 1
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run 5000

‎README.md

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# Benchmarcking Cymbalum against other codes
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This directory contains a way to run the exact same simulation using Cymbalum
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and other molecular simulation codes.

‎data/helium.lmp

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LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.2 on Tue Nov 25 17:43:26 CET 2014
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125 atoms
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0 bonds
4+
0 angles
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0 dihedrals
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0 impropers
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1 atom types
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0 bond types
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0 angle types
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0 dihedral types
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0 improper types
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0.000000 10.000000 xlo xhi
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0.000000 10.000000 ylo yhi
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0.000000 10.000000 zlo zhi
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# Pair Coeffs
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#
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# 1 He
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Masses
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1 4.002600 # He
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Atoms
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1 1 1 0.000000 0.490530 8.413510 0.077726 # He
27+
2 1 1 0.000000 8.837610 3.243840 1.107740 # He
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3 1 1 0.000000 8.443080 0.881072 4.151970 # He
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4 1 1 0.000000 10.103800 2.085110 5.207950 # He
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5 1 1 0.000000 9.790160 0.689489 7.212400 # He
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6 1 1 0.000000 0.678930 1.126350 0.706026 # He
32+
7 1 1 0.000000 8.806070 0.959083 1.306780 # He
33+
8 1 1 0.000000 0.176178 0.904281 2.901610 # He
34+
9 1 1 0.000000 0.675459 3.935810 5.869470 # He
35+
10 1 1 0.000000 -0.091031 2.791920 7.314720 # He
36+
11 1 1 0.000000 9.731100 1.969590 9.091490 # He
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12 1 1 0.000000 9.022440 2.471550 3.031570 # He
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13 1 1 0.000000 0.385359 5.381730 4.301800 # He
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14 1 1 0.000000 1.066970 6.154680 6.045930 # He
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15 1 1 0.000000 9.783260 4.726080 7.897250 # He
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16 1 1 0.000000 7.173460 5.139060 8.159220 # He
42+
17 1 1 0.000000 3.128920 6.394230 1.841040 # He
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18 1 1 0.000000 0.451799 6.903430 2.531340 # He
44+
19 1 1 0.000000 9.741410 7.266470 4.766680 # He
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20 1 1 0.000000 1.825390 4.042470 7.364510 # He
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21 1 1 0.000000 1.464730 5.854790 8.610610 # He
47+
22 1 1 0.000000 8.424080 8.544300 0.450614 # He
48+
23 1 1 0.000000 0.936140 8.884070 3.777740 # He
49+
24 1 1 0.000000 8.550710 8.646080 5.866880 # He
50+
25 1 1 0.000000 6.763000 -0.084194 7.658340 # He
51+
26 1 1 0.000000 1.274330 0.540312 8.664900 # He
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27 1 1 0.000000 9.667350 8.780250 2.014000 # He
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28 1 1 0.000000 -0.020621 10.088300 5.400210 # He
54+
29 1 1 0.000000 2.013430 0.549150 4.354330 # He
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30 1 1 0.000000 2.655120 7.322050 7.470500 # He
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31 1 1 0.000000 2.315780 2.155560 0.982654 # He
57+
32 1 1 0.000000 2.606170 2.229750 3.160500 # He
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33 1 1 0.000000 0.906899 3.642730 3.605920 # He
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34 1 1 0.000000 1.794500 0.517005 6.397280 # He
60+
35 1 1 0.000000 2.106440 2.706090 5.188980 # He
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36 1 1 0.000000 2.486130 4.403120 0.703982 # He
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37 1 1 0.000000 1.560470 5.096100 2.518590 # He
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38 1 1 0.000000 0.961477 3.300900 1.672740 # He
64+
39 1 1 0.000000 3.503110 1.009980 5.625170 # He
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40 1 1 0.000000 1.604890 2.837760 8.961610 # He
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41 1 1 0.000000 0.314200 3.906970 9.836840 # He
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42 1 1 0.000000 1.821320 6.868240 3.986520 # He
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43 1 1 0.000000 1.303270 8.282050 5.755540 # He
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44 1 1 0.000000 2.561160 4.875140 4.762040 # He
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45 1 1 0.000000 4.265250 7.980520 9.070630 # He
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46 1 1 0.000000 2.130750 9.527740 0.320656 # He
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47 1 1 0.000000 1.956530 8.143850 1.777580 # He
73+
48 1 1 0.000000 2.093850 0.303836 2.178180 # He
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49 1 1 0.000000 1.070370 8.710270 7.844160 # He
75+
50 1 1 0.000000 2.389990 7.396620 9.627260 # He
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51 1 1 0.000000 3.742330 8.091860 1.033430 # He
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52 1 1 0.000000 5.607210 1.472940 0.708749 # He
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53 1 1 0.000000 7.625840 7.015390 7.327770 # He
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54 1 1 0.000000 4.641530 9.587170 7.288710 # He
80+
55 1 1 0.000000 6.229100 8.136500 8.437460 # He
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56 1 1 0.000000 5.101300 9.382250 0.449962 # He
82+
57 1 1 0.000000 3.809540 0.060485 3.096360 # He
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58 1 1 0.000000 4.847310 9.678640 4.813310 # He
84+
59 1 1 0.000000 4.421690 1.630260 7.441140 # He
85+
60 1 1 0.000000 2.574290 1.948780 7.377810 # He
86+
61 1 1 0.000000 3.446960 3.807880 8.985350 # He
87+
62 1 1 0.000000 4.436810 2.554440 4.508900 # He
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63 1 1 0.000000 6.031210 3.417610 5.601140 # He
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64 1 1 0.000000 3.713720 3.499050 6.383530 # He
90+
65 1 1 0.000000 3.889300 5.534750 9.515060 # He
91+
66 1 1 0.000000 3.521120 4.104860 2.826920 # He
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67 1 1 0.000000 3.929400 6.007800 3.590970 # He
93+
68 1 1 0.000000 3.125000 6.702620 5.509000 # He
94+
69 1 1 0.000000 3.381000 8.736270 5.675360 # He
95+
70 1 1 0.000000 4.596100 7.573760 6.771610 # He
96+
71 1 1 0.000000 4.932870 5.210930 1.957730 # He
97+
72 1 1 0.000000 4.996390 7.701680 2.600720 # He
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73 1 1 0.000000 3.139900 8.257240 3.602580 # He
99+
74 1 1 0.000000 5.143260 6.793460 0.690854 # He
100+
75 1 1 0.000000 3.030530 9.575750 8.381150 # He
101+
76 1 1 0.000000 6.984410 9.918650 10.313600 # He
102+
77 1 1 0.000000 7.412480 1.828530 9.854020 # He
103+
78 1 1 0.000000 5.751340 9.904690 2.377150 # He
104+
79 1 1 0.000000 6.491020 8.392370 6.425510 # He
105+
80 1 1 0.000000 6.234450 2.279600 7.583770 # He
106+
81 1 1 0.000000 5.424160 2.826100 9.148360 # He
107+
82 1 1 0.000000 3.657680 1.681790 9.260820 # He
108+
83 1 1 0.000000 3.598380 0.638915 1.139320 # He
109+
84 1 1 0.000000 5.991290 1.116540 5.947810 # He
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85 1 1 0.000000 5.871500 4.953550 10.016100 # He
111+
86 1 1 0.000000 6.813700 3.402620 1.054140 # He
112+
87 1 1 0.000000 4.529270 1.885730 2.531730 # He
113+
88 1 1 0.000000 6.879850 1.735850 2.246340 # He
114+
89 1 1 0.000000 7.457860 4.395730 2.961640 # He
115+
90 1 1 0.000000 5.205430 4.313410 7.754730 # He
116+
91 1 1 0.000000 4.585470 3.366750 1.129230 # He
117+
92 1 1 0.000000 6.634200 6.101660 1.884860 # He
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93 1 1 0.000000 5.644010 3.506460 3.072080 # He
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94 1 1 0.000000 4.673290 4.899980 5.443120 # He
120+
95 1 1 0.000000 5.423150 6.266530 8.537550 # He
121+
96 1 1 0.000000 7.783070 6.892210 9.750090 # He
122+
97 1 1 0.000000 7.285690 7.765860 3.178320 # He
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98 1 1 0.000000 5.371250 7.338130 4.657580 # He
124+
99 1 1 0.000000 5.946210 5.761280 3.729250 # He
125+
100 1 1 0.000000 5.490590 0.497117 8.908890 # He
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101 1 1 0.000000 8.860070 0.164228 9.208390 # He
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102 1 1 0.000000 6.667150 8.083280 1.364910 # He
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103 1 1 0.000000 7.762920 9.675050 2.449480 # He
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104 1 1 0.000000 7.478350 2.771700 4.399700 # He
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105 1 1 0.000000 8.151640 0.880297 6.020500 # He
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106 1 1 0.000000 8.121190 3.516930 8.790840 # He
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107 1 1 0.000000 5.785540 1.173430 3.853690 # He
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108 1 1 0.000000 7.151320 4.896090 5.075300 # He
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109 1 1 0.000000 8.994840 3.947900 4.574850 # He
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110 1 1 0.000000 7.986130 1.460740 8.038470 # He
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111 1 1 0.000000 8.284070 5.054410 0.610514 # He
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112 1 1 0.000000 9.638570 4.793300 2.185080 # He
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113 1 1 0.000000 8.569110 6.079890 3.469690 # He
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114 1 1 0.000000 9.004270 5.834360 6.087140 # He
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115 1 1 0.000000 7.719530 3.531060 6.617260 # He
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116 1 1 0.000000 9.621440 6.022850 9.489640 # He
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117 1 1 0.000000 8.574710 6.983590 1.522430 # He
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118 1 1 0.000000 7.467520 7.060260 5.176540 # He
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119 1 1 0.000000 3.394500 5.486060 7.203840 # He
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120 1 1 0.000000 9.932590 6.951050 7.754760 # He
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121 1 1 0.000000 1.478160 5.990950 0.532806 # He
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122 1 1 0.000000 9.101030 8.916060 3.976370 # He
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123 1 1 0.000000 6.988920 9.321330 4.487070 # He
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124 1 1 0.000000 5.931760 6.096550 6.430180 # He
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125 1 1 0.000000 8.579510 8.657120 8.066780 # He
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‎data/helium.xyz

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125
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Initial configuration for Lennard-Jone fluid simulation
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He 0.49053 8.41351 0.0777257
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He 8.83761 3.24384 1.10774
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He 8.44308 0.881072 4.15197
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He 10.1038 2.08511 5.20795
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He 9.79016 0.689489 7.2124
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He 0.67893 1.12635 0.706026
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He 8.80607 0.959083 1.30678
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He 0.176178 0.904281 2.90161
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He 0.675459 3.93581 5.86947
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He -0.0910313 2.79192 7.31472
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He 9.7311 1.96959 9.09149
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He 9.02244 2.47155 3.03157
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He 0.385359 5.38173 4.3018
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He 1.06697 6.15468 6.04593
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He 9.78326 4.72608 7.89725
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He 7.17346 5.13906 8.15922
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He 3.12892 6.39423 1.84104
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He 0.451799 6.90343 2.53134
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He 9.74141 7.26647 4.76668
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He 1.82539 4.04247 7.36451
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He 1.46473 5.85479 8.61061
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He 8.42408 8.5443 0.450614
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He 0.93614 8.88407 3.77774
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He 8.55071 8.64608 5.86688
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He 6.763 -0.0841943 7.65834
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He 1.27433 0.540312 8.6649
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He 9.66735 8.78025 2.014
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He -0.0206213 10.0883 5.40021
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He 2.01343 0.54915 4.35433
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He 2.65512 7.32205 7.4705
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He 2.31578 2.15556 0.982654
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He 2.60617 2.22975 3.1605
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He 0.906899 3.64273 3.60592
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He 1.7945 0.517005 6.39728
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He 2.10644 2.70609 5.18898
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He 2.48613 4.40312 0.703982
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He 1.56047 5.0961 2.51859
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He 0.961477 3.3009 1.67274
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He 3.50311 1.00998 5.62517
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He 1.60489 2.83776 8.96161
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He 0.3142 3.90697 9.83684
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He 1.82132 6.86824 3.98652
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He 1.30327 8.28205 5.75554
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He 2.56116 4.87514 4.76204
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He 4.26525 7.98052 9.07063
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He 2.13075 9.52774 0.320656
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He 1.95653 8.14385 1.77758
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He 2.09385 0.303836 2.17818
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He 1.07037 8.71027 7.84416
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He 2.38999 7.39662 9.62726
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He 3.74233 8.09186 1.03343
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He 5.60721 1.47294 0.708749
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He 7.62584 7.01539 7.32777
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He 4.64153 9.58717 7.28871
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He 6.2291 8.1365 8.43746
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He 5.1013 9.38225 0.449962
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He 3.80954 0.0604853 3.09636
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He 4.84731 9.67864 4.81331
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He 4.42169 1.63026 7.44114
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He 2.57429 1.94878 7.37781
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He 3.44696 3.80788 8.98535
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He 4.43681 2.55444 4.5089
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He 6.03121 3.41761 5.60114
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He 3.71372 3.49905 6.38353
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He 3.8893 5.53475 9.51506
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He 3.52112 4.10486 2.82692
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He 3.9294 6.0078 3.59097
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He 3.125 6.70262 5.509
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He 3.381 8.73627 5.67536
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He 4.5961 7.57376 6.77161
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He 4.93287 5.21093 1.95773
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He 4.99639 7.70168 2.60072
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He 3.1399 8.25724 3.60258
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He 5.14326 6.79346 0.690854
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He 3.03053 9.57575 8.38115
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He 6.98441 9.91865 10.3136
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He 7.41248 1.82853 9.85402
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He 5.75134 9.90469 2.37715
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He 6.49102 8.39237 6.42551
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He 6.23445 2.2796 7.58377
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He 5.42416 2.8261 9.14836
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He 3.65768 1.68179 9.26082
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He 3.59838 0.638915 1.13932
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He 5.99129 1.11654 5.94781
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He 5.8715 4.95355 10.0161
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He 6.8137 3.40262 1.05414
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He 4.52927 1.88573 2.53173
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He 6.87985 1.73585 2.24634
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He 7.45786 4.39573 2.96164
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He 5.20543 4.31341 7.75473
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He 4.58547 3.36675 1.12923
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He 6.6342 6.10166 1.88486
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He 5.64401 3.50646 3.07208
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He 4.67329 4.89998 5.44312
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He 5.42315 6.26653 8.53755
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He 7.78307 6.89221 9.75009
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He 7.28569 7.76586 3.17832
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He 5.37125 7.33813 4.65758
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He 5.94621 5.76128 3.72925
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He 5.49059 0.497117 8.90889
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He 8.86007 0.164228 9.20839
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He 6.66715 8.08328 1.36491
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He 7.76292 9.67505 2.44948
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He 7.47835 2.7717 4.3997
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He 8.15164 0.880297 6.0205
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He 8.12119 3.51693 8.79084
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He 5.78554 1.17343 3.85369
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He 7.15132 4.89609 5.0753
111+
He 8.99484 3.9479 4.57485
112+
He 7.98613 1.46074 8.03847
113+
He 8.28407 5.05441 0.610514
114+
He 9.63857 4.7933 2.18508
115+
He 8.56911 6.07989 3.46969
116+
He 9.00427 5.83436 6.08714
117+
He 7.71953 3.53106 6.61726
118+
He 9.62144 6.02285 9.48964
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He 8.57471 6.98359 1.52243
120+
He 7.46752 7.06026 5.17654
121+
He 3.3945 5.48606 7.20384
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He 9.93259 6.95105 7.75476
123+
He 1.47816 5.99095 0.532806
124+
He 9.10103 8.91606 3.97637
125+
He 6.98892 9.32133 4.48707
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He 5.93176 6.09655 6.43018
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He 8.57951 8.65712 8.06678

‎helium.rs

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extern crate cymbalum;
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use cymbalum::*;
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use std::path::Path;
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#[test]
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fn main() {
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Logger::stdout();
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let data_dir = Path::new(file!()).parent().unwrap();
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let configuration = data_dir.join("data").join("helium.xyz");
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let mut system = System::from_file(configuration.to_str().unwrap()).unwrap();
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system.set_cell(UnitCell::cubic(10.0));
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system.add_pair_interaction("He", "He",
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LennardJones{
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sigma: units::from(2.0, "A").unwrap(),
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epsilon: units::from(0.3, "kJ/mol").unwrap()
17+
}
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);
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let mut velocities = BoltzmanVelocities::new(units::from(300.0, "K").unwrap());
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velocities.seed(42);
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velocities.init(&mut system);
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let mut simulation = Simulation::new(
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MolecularDynamics::new(units::from(1.0, "fs").unwrap())
26+
);
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simulation.run(&mut system, 5000);
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}

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