polychrom-reporter

Untitled.ipynb

{
  "cells": [
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "import polychrom\nimport numpy as np \nimport h5py \nfrom polychrom.simulation import Simulation\nimport polychrom.starting_conformations\nimport polychrom.forces, polychrom.forcekits\nimport simtk.openmm \nimport os \nimport shutil",
      "execution_count": 1,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "\n\ndef convert_to_hdf5_array(data):\n    if type(data) == str:\n        data = np.array(data, dtype=\"S\")\n\n\n    data = np.array(data)\n    return data\n        \n\n\nclass dummyReporter(object):\n    def __init__(self, folder, max_data_length=20):\n        if not os.path.exists(folder):\n            os.mkdir(folder)\n        if len(os.listdir(folder)) != 0:\n            raise RuntimeError(f\"folder {folder} is not empty\")\n        self.counter = {}\n        self.datas = {}\n        self.max_data_length = max_data_length\n        self.folder = folder\n\n    def report(self, name, values):\n        count = self.counter.get(name, 0)\n        \n        if name not in [\"data\"]:\n            filename = f\"{name}_{count}.hdf5\"\n            with h5py.File(os.path.join(self.folder,filename)) as file: \n                for dsetname, data in values.items():\n                    file.create_dataset(dsetname, data=convert_to_hdf5_array(data))\n                \n                \n        else:\n            self.datas[count] = values \n            if len(self.datas) == self.max_data_length:\n                self.dump_data()\n        self.counter[name] = count + 1\n                \n                \n    def dump_data(self):\n        if len(self.datas) > 0:\n            cmin = min(self.datas.keys())\n            cmax = max(self.datas.keys())\n            filename = f\"data_{cmin}-{cmax}.hdf5\"\n            print(filename)\n            with h5py.File(os.path.join(self.folder,filename)) as file: \n                for count, values in self.datas.items(): \n                    gr = file.create_group(str(count))\n                    for dsetname, data in values.items():\n                        gr.create_dataset(dsetname, data=convert_to_hdf5_array(data))\n            self.datas = {}\n\n            \n                \n",
      "execution_count": 2,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "%rm  test/*\ndata = polychrom.starting_conformations.grow_cubic(1000,30)\nreporter = dummyReporter(folder=\"test\", max_data_length=5)\n\nsim = Simulation(N=1000, error_tol=0.001, collision_rate=0.01, integrator =\"variableLangevin\", platform=\"CPU\", \n                reporters=[reporter])\nsim.setData(data)\nsim.addForce(polychrom.forcekits.polymerChains(sim))\nsim._applyForces()\nsim.addForce(polychrom.forces.sphericalConfinement(sim, density=0.1))\nfor i in range(20):\n    sim.doBlock(10)\nreporter.dump_data()\n",
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "text": "INFO:root:adding force HarmonicBonds 0\nINFO:root:adding force Angle 1\nINFO:root:adding force PolynomialRepulsive 2\nINFO:root:Particles loaded. Potential energy is 0.051877\nINFO:root:block    1 pos[1]=[13.9 13.7 13.9] dr=0.21 t=0.9ps kin=8.80 pot=4.40 Rg=5.488 dt=23.1fs dx=15.29pm \nINFO:root:block    2 pos[1]=[13.9 13.7 13.8] dr=0.18 t=1.1ps kin=4.33 pot=9.45 Rg=5.488 dt=20.2fs dx=9.41pm \nINFO:root:block    3 pos[1]=[13.9 13.6 13.8] dr=0.08 t=1.3ps kin=7.99 pot=5.78 Rg=5.492 dt=19.6fs dx=12.34pm \nINFO:root:block    4 pos[1]=[13.8 13.5 13.8] dr=0.15 t=1.6ps kin=6.96 pot=6.93 Rg=5.500 dt=21.7fs dx=12.81pm \nINFO:root:block    5 pos[1]=[13.8 13.5 13.8] dr=0.11 t=1.8ps kin=7.41 pot=6.47 Rg=5.508 dt=21.0fs dx=12.78pm \nINFO:root:block    6 pos[1]=[13.8 13.5 13.8] dr=0.13 t=2.0ps kin=7.83 pot=6.03 Rg=5.515 dt=21.0fs dx=13.14pm \nINFO:root:block    7 pos[1]=[13.8 13.4 13.8] dr=0.12 t=2.2ps kin=7.52 pot=6.30 Rg=5.522 dt=21.0fs dx=12.88pm \n",
          "name": "stderr"
        },
        {
          "output_type": "stream",
          "text": "Exclude neighbouring chain particles from PolynomialRepulsive\nNumber of exceptions: 999\ndata_0-4.hdf5\n",
          "name": "stdout"
        },
        {
          "output_type": "stream",
          "text": "INFO:root:block    8 pos[1]=[13.7 13.4 13.9] dr=0.12 t=2.4ps kin=7.85 pot=5.95 Rg=5.532 dt=21.0fs dx=13.16pm \nINFO:root:block    9 pos[1]=[13.7 13.4 13.9] dr=0.13 t=2.6ps kin=8.02 pot=5.75 Rg=5.542 dt=21.0fs dx=13.30pm \nINFO:root:block   10 pos[1]=[13.6 13.3 13.9] dr=0.13 t=2.8ps kin=7.73 pot=6.03 Rg=5.552 dt=21.0fs dx=13.05pm \nINFO:root:block   11 pos[1]=[13.6 13.3 13.9] dr=0.12 t=3.0ps kin=7.58 pot=6.16 Rg=5.564 dt=21.0fs dx=12.93pm \nINFO:root:block   12 pos[1]=[13.6 13.2 13.9] dr=0.13 t=3.3ps kin=8.30 pot=5.42 Rg=5.577 dt=21.0fs dx=13.53pm \nINFO:root:block   13 pos[1]=[13.6 13.2 13.8] dr=0.13 t=3.5ps kin=7.68 pot=6.02 Rg=5.590 dt=21.0fs dx=13.02pm \nINFO:root:block   14 pos[1]=[13.7 13.2 13.8] dr=0.13 t=3.7ps kin=8.12 pot=5.55 Rg=5.604 dt=21.0fs dx=13.38pm \nINFO:root:block   15 pos[1]=[13.8 13.1 13.7] dr=0.13 t=3.9ps kin=8.11 pot=5.52 Rg=5.618 dt=21.0fs dx=13.37pm \nINFO:root:block   16 pos[1]=[13.8 13.1 13.7] dr=0.13 t=4.1ps kin=7.89 pot=5.72 Rg=5.634 dt=21.0fs dx=13.19pm \nINFO:root:block   17 pos[1]=[13.7 12.9 13.7] dr=0.13 t=4.3ps kin=7.61 pot=6.00 Rg=5.650 dt=21.0fs dx=12.95pm \nINFO:root:block   18 pos[1]=[13.7 12.9 13.6] dr=0.13 t=4.5ps kin=8.20 pot=5.37 Rg=5.667 dt=21.0fs dx=13.44pm \nINFO:root:block   19 pos[1]=[13.9 12.8 13.6] dr=0.13 t=4.7ps kin=7.74 pot=5.80 Rg=5.685 dt=21.0fs dx=13.06pm \nINFO:root:block   20 pos[1]=[14.0 12.8 13.6] dr=0.12 t=4.9ps kin=7.83 pot=5.70 Rg=5.703 dt=21.0fs dx=13.14pm \n",
          "name": "stderr"
        },
        {
          "output_type": "stream",
          "text": "data_5-9.hdf5\ndata_10-14.hdf5\ndata_15-19.hdf5\n",
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "ls test",
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "text": "\u001b[0m\u001b[38;5;202mapplied_forces_0.hdf5\u001b[0m*  \u001b[38;5;202mdata_10-14.hdf5\u001b[0m*  \u001b[38;5;202mdata_5-9.hdf5\u001b[0m*\r\n\u001b[38;5;202mdata_0-4.hdf5\u001b[0m*          \u001b[38;5;202mdata_15-19.hdf5\u001b[0m*  \u001b[38;5;202mload_data_0.hdf5\u001b[0m*\r\n",
          "name": "stdout"
        }
      ]
    }
  ],
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      "name": "python3",
      "display_name": "Python 3",
      "language": "python"
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      "mimetype": "text/x-python",
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
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      "pygments_lexer": "ipython3",
      "nbconvert_exporter": "python",
      "file_extension": ".py"
    },
    "gist": {
      "id": "838ad1a2a43ca84aca8856999214c0ed",
      "data": {
        "description": "polychrom-reporter",
        "public": true
      }
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    "_draft": {
      "nbviewer_url": "https://gist.github.com/838ad1a2a43ca84aca8856999214c0ed"
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