{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "8a365a14",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "# Switch calculation engine\n",
    "This notebook shows how we can switch calculation engine (external crystallographic library) and calculate diffraction profile using constant wavelength experiment type."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9ecc4733",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "# EasyScience, technique-independent\n",
    "from easyCore import np\n",
    "from easyCore.Fitting.Fitting import Fitter\n",
    "\n",
    "# EasyScience, diffraction\n",
    "from easyDiffractionLib import Site, Phase, Phases\n",
    "from easyDiffractionLib.Jobs import Powder1DCW, InterfaceFactory\n",
    "\n",
    "# Vizualization\n",
    "import py3Dmol\n",
    "from bokeh.io import show, output_notebook\n",
    "from bokeh.plotting import figure\n",
    "\n",
    "# Misc\n",
    "import xarray as xr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d76d50fc",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "output_notebook()\n",
    "FIGURE_WIDTH = 700\n",
    "FIGURE_HEIGHT = 300"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "283767f9",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Sample"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "19a39b25",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "### Create an atom using `Site` interface"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "41020330",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "atom = Site.from_pars(label=\"Cl\",\n",
    "                      specie=\"Cl\",\n",
    "                      fract_x=0.0,\n",
    "                      fract_y=0.0,\n",
    "                      fract_z=0.0)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "910aed87",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "### Create a phase, set space group, add atom"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1e2f3193",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "phase = Phase(name=\"salt\")\n",
    "\n",
    "phase.spacegroup.space_group_HM_name = \"F m -3 m\"\n",
    "\n",
    "phase.add_atom(atom)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d4532d8b",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "### Add another atom (using `Phase` interface)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4231d16a",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "phase.add_atom('Na', 'Na', 0.5, 0.5, 0.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "81ace320",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "### Visualise the structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e68ddbea",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "viewer = py3Dmol.view()\n",
    "viewer.addModel(phase.to_cif_str(),'cif',{'doAssembly':True,'duplicateAssemblyAtoms':True,'normalizeAssembly':True})\n",
    "viewer.setStyle({'sphere':{'colorscheme':'Jmol','scale':.2},'stick':{'colorscheme':'Jmol', 'radius': 0.1}})\n",
    "viewer.addUnitCell()\n",
    "viewer.replicateUnitCell(2,2,2)\n",
    "viewer.zoomTo()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ebe0e0ee",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "### Create Phases object"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "29071aa2",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "phases = Phases()\n",
    "phases.append(phase)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "07db27b5",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Experiment"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dd0fce50",
   "metadata": {},
   "source": [
    "### Create `Dataset`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "df64aa80",
   "metadata": {},
   "outputs": [],
   "source": [
    "data = xr.Dataset()\n",
    "x_data = np.linspace(20, 170, 500)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2d961469",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "### Create `Job`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b4ffa97b",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "job = Powder1DCW('NaCl', data, phases=phases)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "784fb8e5",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "print(f\"Current calculator engine: {job.interface.current_interface_name}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "210bc79d",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "print(f\"Available calculator engines: {job.interface.available_interfaces}\")\n",
    "print(f\"Available calculators for CW: {job.interface.interface_compatability('Npowder1DCWunp')}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e93c42b9",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "###  Modify instrumental parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "83e3845f",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "job.parameters.resolution_u = 0.1447\n",
    "job.parameters.resolution_v = -0.4252\n",
    "job.parameters.resolution_w = 0.3864\n",
    "job.parameters.resolution_x = 0.0\n",
    "job.parameters.resolution_y = 0.0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "370f0baa",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "###  Modify pattern parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "70fa1571",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "job.pattern.zero_shift = 0.0\n",
    "job.pattern.scale = 100.0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "eb234f76",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Simulation"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "00e24eab",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "### Calculate the profile using the default calculation engine"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "91df1925",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "_ = job.create_simulation(x_data)\n",
    "y_data_cryspy = np.array(data['sim_NaCl'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "05ab7ef9",
   "metadata": {},
   "outputs": [],
   "source": [
    "print(\"some Ycalc from CrysPy:\\n\", y_data_cryspy[315:330])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f556cc94",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "fig = figure(width=FIGURE_WIDTH, height=FIGURE_HEIGHT)\n",
    "fig.line(x_data, y_data_cryspy, legend_label='CW Simulation', color='orangered', line_width=2)\n",
    "show(fig)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c9a336a8",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "###  Switch calculator"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "eeeb243b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# The following code generates AttributeError\n",
    "#calculator.switch('CrysFML')\n",
    "#_ = job.create_simulation(x_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "20c3ce77",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "# Temporary workaround\n",
    "job.interface = InterfaceFactory(interface_name='CrysFML')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d6012853",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "print(f\"Current calculator engine: {job.interface.current_interface_name}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "271bf903",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Simulation"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0c0b9ac4",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "### Calculate the profile using the calculator engine just selected"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e03a750e",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "_ = job.create_simulation(x_data)\n",
    "y_data_crysfml = np.array(data['sim_NaCl'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "70544360",
   "metadata": {},
   "outputs": [],
   "source": [
    "print(\"some Ycalc from CrysFML:\\n\", y_data_crysfml[315:330])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "071a29ea",
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "fig = figure(width=FIGURE_WIDTH, height=FIGURE_HEIGHT)\n",
    "fig.line(x_data, y_data_crysfml, legend_label='CW Simulation', color='olivedrab', line_width=2)\n",
    "show(fig)"
   ]
  }
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