Notes on OpenPMD https://www.openpmd.org/#/start

OpenPMD2D.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<HDF5 file \"data00000255.h5\" (mode r+)>"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import h5py\n",
    "f = h5py.File(\"data00000255.h5\")\n",
    "f"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['data']"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(f.keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['255']"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(f['data'].keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['fields', 'particles']"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(f['data']['255'].keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['E', 'rho']"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(f['data']['255']['fields'].keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['x', 'y', 'z']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(f['data']['255']['fields']['E'].keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<HDF5 dataset \"rho\": shape (51, 201), type \"<f8\">"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "f['data']['255']['fields']['rho']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(51, 201)"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "f['data']['255']['fields']['rho'].shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['unitSI',\n",
       " 'position',\n",
       " 'unitDimension',\n",
       " 'timeOffset',\n",
       " 'geometry',\n",
       " 'gridSpacing',\n",
       " 'axisLabels',\n",
       " 'gridGlobalOffset',\n",
       " 'dataOrder',\n",
       " 'gridUnitSI',\n",
       " 'fieldSmoothing']"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rho = f['data']['255']['fields']['rho']\n",
    "list(rho.attrs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'unitSI': 1.0,\n",
       " 'position': array([0., 0.]),\n",
       " 'unitDimension': array([-3.,  0.,  1.,  1.,  0.,  0.,  0.]),\n",
       " 'timeOffset': 0.0,\n",
       " 'geometry': b'cartesian',\n",
       " 'gridSpacing': array([6.e-07, 1.e-07]),\n",
       " 'axisLabels': array([b'x', b'z'], dtype='|S1'),\n",
       " 'gridGlobalOffset': array([-1.50e-05,  1.02e-05]),\n",
       " 'dataOrder': b'C',\n",
       " 'gridUnitSI': 1.0,\n",
       " 'fieldSmoothing': b'none'}"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dict(rho.attrs.items())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'unitDimension': array([ 1.,  1., -3., -1.,  0.,  0.,  0.]),\n",
       " 'timeOffset': 0.0,\n",
       " 'geometry': b'cartesian',\n",
       " 'gridSpacing': array([6.e-07, 1.e-07]),\n",
       " 'axisLabels': array([b'x', b'z'], dtype='|S1'),\n",
       " 'gridGlobalOffset': array([-1.50e-05,  1.02e-05]),\n",
       " 'dataOrder': b'C',\n",
       " 'gridUnitSI': 1.0,\n",
       " 'fieldSmoothing': b'none'}"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "E = f['data']['255']['fields']['E']\n",
    "dict(E.attrs.items())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(51, 201)"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "E['x'].shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Attributes of HDF5 object at 139982125851224>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "E['x'].attrs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'meshesPath': b'fields/',\n",
       " 'softwareVersion': b'4',\n",
       " 'date': b'2018-02-06 09:36:49 -0800',\n",
       " 'openPMD': b'1.1.0',\n",
       " 'software': b'warp',\n",
       " 'iterationFormat': b'data%T.h5',\n",
       " 'basePath': b'/data/%T/',\n",
       " 'particlesPath': b'particles/',\n",
       " 'openPMDextension': 1,\n",
       " 'iterationEncoding': b'fileBased'}"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dict(f.attrs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'unitSI': 1.0,\n",
       " 'position': array([0., 0.]),\n",
       " 'unitDimension': array([-3.,  0.,  1.,  1.,  0.,  0.,  0.]),\n",
       " 'timeOffset': 0.0,\n",
       " 'geometry': b'cartesian',\n",
       " 'gridSpacing': array([6.e-07, 1.e-07]),\n",
       " 'axisLabels': array([b'x', b'z'], dtype='|S1'),\n",
       " 'gridGlobalOffset': array([-1.50e-05,  1.02e-05]),\n",
       " 'dataOrder': b'C',\n",
       " 'gridUnitSI': 1.0,\n",
       " 'fieldSmoothing': b'none'}"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dict(rho.attrs)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}

OpenPMDNotes.md

OpenPMD notes

Fields, spatial quantities are records.

Position.x - a component of a record.

Each record has attributes:

• unitSI (conversion factor)
• unitDimension (dimensionality)
  • Powers of SI - https://www.openpmd.org/#/step-12
    • easy to transform that into units!
• time/timeUnitSI

Squashing constant data

Provide a common interface (.value, .unitSI, .shape) for arrays and constants via treating the latter like hdf5 groups.

Charge-as-an-array:

• particles (group)
  • electrons (group):
    • charge (array)
      • unitSI (attribut)

Charge-an-a-group:

• particles (group)
  • electrons (group):
    • charge (group)
      • value (attribute, float)
      • unitSI (attribute)
      • shape (attribute)

For Cartesian 2D (z=const) you can have z-as-a-group.

Existing tools:

• openPMD Viewer
  • has Python API apparently
• Has a API at https://github.com/openPMD/openPMD-api

neat Zenodo poster

https://zenodo.org/record/822396

Also:

• this twitter thread https://twitter.com/StanczakDominik/status/1007310404886978563?s=19