depletion.ipynb

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    "import util\n",
    "import os\n",
    "from IPython.core.display import Markdown\n",
    "benchmark = 'depletion'"
   ]
  },
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      "text/markdown": [
       "# depletion benchmark\n",
       "\n",
       "The depletion benchmark runs a system of $1000$ cuboctahedra, with depletants at a size ratio $q=0.25$ and a reservoir density of $\\phi_{dep}^r=0.80$.\n",
       "\n",
       "Under these conditions, the cuboctahedra forms a dense sheared BCC crystal. The depletion method was described in:\n",
       "[Glaser, J et al. A parallel algorithm for implicit depletant simulations. Journal of Chemical Physics, 2015.](http://scitation.aip.org/content/aip/journal/jcp/143/18/10.1063/1.4935175)\n",
       "The cuboctahedra with depletion system was studied in the research article:\n",
       "[Karas AS et al. Using depletion to control colloidal crystal assemblies of hard cuboctahedra. Soft Matter, 2015](http://pubs.rsc.org/en/content/articlelanding/2016/sm/c6sm00620e)\n",
       "\n",
       "<img src=\"depletion/depletion.png\" style=\"width: 280px;\"/>\n",
       "\n",
       "Parameters:\n",
       "\n",
       "* $N = 1000$\n",
       "* Hard particle Monte Carlo\n",
       "    * Polyhedron Vertices: [[-0.53139075, -0.53139075, 0], [-0.53139075, 0.53139075, 0], [0.53139075, -0.53139075, 0], [0.53139075, 0.53139075, 0], [0, -0.53139075, -0.531390750], [0, -0.53139075, 0.53139075], [0, 0.53139075, -0.53139075], [0, 0.53139075, 0.53139075], [-0.53139075, 0, -0.53139075], [-0.53139075, 0, 0.53139075], [0.53139075, 0, -0.53139075], [0.53139075, 0, 0.53139075]]\n",
       "    * Polyhedron sweep radius: 0\n",
       "    * Depletant vertices: []\n",
       "    * Depletant sweep radius: $0.7515*0.25 = 0.1879$\n",
       "    * $d = 0.0351 $\n",
       "    * $a = 0.0544 $\n",
       "    * implicit = True\n",
       "    * $nR = 28.8 $\n",
       "    * ntrial = 0\n",
       "* Log file period: 10000 time steps\n",
       "\n"
      ],
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     "execution_count": 3,
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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 Monte Carlo sweeps, where one sweep is N trial moves."
   ]
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   "execution_count": 4,
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      "text/markdown": [
       "| 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 | 1,000 |  Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz | **Tesla P100-PCIE-16GB** | 1 | 19.92 |\n",
       "| 2016/10/23 | psg | gcc 4.8.5 | 8.0 | 2.1.1 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla P100-PCIE-16GB** | 1 | 13.44 |\n",
       "| 2016/10/23 | psg | gcc 4.8.5 | 8.0 | 2.1.1 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla K80** | 1 | 27.39 |\n",
       "| 2016/10/23 | psg | gcc 4.8.5 | 8.0 | 2.1.1 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla M40 24GB** | 1 | 28.61 |\n",
       "| 2016/10/23 | psg | gcc 4.8.5 | 8.0 | 2.1.1 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla K40m** | 1 | 39.16 |\n",
       "| 2016/10/12 | psg | gcc 4.8.5 | 8.0 | 2.1.0 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla P100-PCIE-16GB** | 1 | 13.77 |\n",
       "| 2016/10/13 | psg | gcc 4.8.5 | 7.5 | 2.1.0 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla M40 24GB** | 1 | 27.69 |\n",
       "| 2016/10/12 | psg | gcc 4.8.5 | 8.0 | 2.1.0 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla K80** | 1 | 29.23 |\n",
       "| 2016/10/13 | psg | gcc 4.8.5 | 7.5 | 2.1.0 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz | **Tesla K40m** | 1 | 39.32 |\n",
       "| 2016/09/13 | collins | gcc 4.8.5 | 7.5 | 2.0.3 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **TITAN X** | 1 | 15.95 |\n",
       "| 2016/09/13 | collins | gcc 4.8.5 | 7.5 | 2.0.3 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Quadro M6000** | 1 | 29.01 |\n",
       "| 2016/09/13 | collins | gcc 4.8.5 | 7.5 | 2.0.3 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **Tesla K40c** | 1 | 33.97 |\n",
       "| 2016/09/13 | collins | gcc 4.8.5 | 7.5 | 2.0.3 | double | 1,000 |  Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz | **GeForce GTX 680** | 1 | 37.28 |\n"
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    "rows = util.read_rows(benchmark)\n",
    "table = util.make_table(rows)\n",
    "Markdown(table)"
   ]
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