quasicrystal.ipynb

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    "import util\n",
    "import os\n",
    "from IPython.core.display import Markdown\n",
    "benchmark = 'quasicrystal'"
   ]
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      "text/markdown": [
       "# quasicrystal benchmark\n",
       "\n",
       "The quasicrystal benchmark runs a system of particles with an oscillatory pair potential that forms an icosahedral\n",
       "quasicrystal. This model is used in the research article:\n",
       "[Engel M, et. al. (2015) Computational self-assembly of a one-component icosahedral quasicrystal, Nature materials 14(January), p. 109-116,](http://dx.doi.org/10.1038/NMAT4152)\n",
       "\n",
       "<img src=\"quasicrystal/quasicrystal.jpeg\" style=\"width: 280px;\"/>\n",
       "\n",
       "Parameters:\n",
       "\n",
       "* $N = 100000$\n",
       "* $\\rho = 0.03$\n",
       "* Tabulated pair force\n",
       "    * $$V = \\frac{1}{r^{15}} + \\frac{\\cos(k (r - 1.25) - \\phi)}{r^3}$$\n",
       "    * $k = 6.25$\n",
       "    * $\\phi = 0.62$\n",
       "* Integration: Nos&eacute;-Hoover NVT\n",
       "    * $T=0.18$\n",
       "    * $\\tau=1.0$\n",
       "    * $\\delta t = 0.01$\n"
      ],
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   "source": [
    "Markdown(open(os.path.join(benchmark, 'README.md'), 'r').read())"
   ]
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   "source": [
    "## Performance data\n",
    "\n",
    "Performance results are reported in hours to complete ten million time steps."
   ]
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       "| Date | System | Compiler | CUDA | HOOMD | Precision | N | CPU | GPU | Ranks | Time for 10e6 steps (hours)|\n",
       "|------|--------|----------|------|-------|-----------|---|-----|-----|-------|---------------:|\n",
       "| 2018/01/15 | comet | gcc 4.9.2 | 8.0 | 2.2.2 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz | **Tesla P100-PCIE-16GB** | 1 | 3.45 |\n",
       "| 2016/10/23 | psg | gcc 4.8.5 | 8.0 | 2.1.1 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla P100-PCIE-16GB** | 1 | 3.27 |\n",
       "| 2016/10/23 | psg | gcc 4.8.5 | 8.0 | 2.1.1 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla K80** | 1 | 10.07 |\n",
       "| 2016/10/23 | psg | gcc 4.8.5 | 8.0 | 2.1.1 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla K40m** | 1 | 10.93 |\n",
       "| 2016/10/23 | psg | gcc 4.8.5 | 8.0 | 2.1.1 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla M40 24GB** | 1 | 18.58 |\n",
       "| 2016/10/12 | psg | gcc 4.8.5 | 8.0 | 2.1.0 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla P100-PCIE-16GB** | 1 | 3.34 |\n",
       "| 2016/10/12 | psg | gcc 4.8.5 | 8.0 | 2.1.0 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla K80** | 1 | 10.22 |\n",
       "| 2016/10/13 | psg | gcc 4.8.5 | 7.5 | 2.1.0 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla K40m** | 1 | 11.64 |\n",
       "| 2016/10/13 | psg | gcc 4.8.5 | 7.5 | 2.1.0 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla M40 24GB** | 1 | 19.53 |\n",
       "| 2016/09/13 | collins | gcc 4.8.5 | 7.5 | 2.0.3 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla K40c** | 1 | 10.27 |\n",
       "| 2016/09/13 | collins | gcc 4.8.5 | 7.5 | 2.0.3 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **TITAN X** | 1 | 11.28 |\n",
       "| 2016/09/13 | collins | gcc 4.8.5 | 7.5 | 2.0.3 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Quadro M6000** | 1 | 21.24 |\n",
       "| 2016/09/13 | collins | gcc 4.8.5 | 7.5 | 2.0.3 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **GeForce GTX 680** | 1 | 31.29 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.3.0 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Quadro M6000** | 1 | 5.51 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.3.0 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla K40c** | 1 | 8.28 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.3.0 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla K40c** | 1 | 10.70 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.3.0 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **GeForce GTX 680** | 1 | 15.79 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.3.0 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Quadro M6000** | 1 | 22.75 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.3.0 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla C2070** | 1 | 23.29 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.3.0 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla C2070** | 1 | 31.43 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.3.0 | double | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **GeForce GTX 680** | 1 | 32.27 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.2.1 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Quadro M6000** | 1 | 5.23 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.2.1 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla K40c** | 1 | 8.45 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.2.1 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **GeForce GTX 680** | 1 | 16.18 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.2.1 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla C2070** | 1 | 23.54 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.1.1 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Quadro M6000** | 1 | 3.18 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.1.1 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla K40c** | 1 | 4.84 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.1.1 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **GeForce GTX 680** | 1 | 7.05 |\n",
       "| 2015/12/14 | collins | gcc 4.9.3 | 7.5 | 1.1.1 | single | 100,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla C2070** | 1 | 13.05 |\n"
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    "rows = util.read_rows(benchmark)\n",
    "table = util.make_table(rows)\n",
    "Markdown(table)"
   ]
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