{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "# AtomsBase integration"
   ],
   "metadata": {}
  },
  {
   "cell_type": "markdown",
   "source": [
    "[AtomsBase.jl](https://github.com/JuliaMolSim/AtomsBase.jl) is a common interface\n",
    "for representing atomic structures in Julia. DFTK directly supports using such\n",
    "structures to run a calculation as is demonstrated here."
   ],
   "metadata": {}
  },
  {
   "outputs": [
    {
     "output_type": "execute_result",
     "data": {
      "text/plain": "FlexibleSystem(Si₂, AtomsBase.Periodic, box=[[0.0, 5.13, 5.13], [5.13, 0.0, 5.13], [5.13, 5.13, 0.0]]u\"a₀\")"
     },
     "metadata": {},
     "execution_count": 1
    }
   ],
   "cell_type": "code",
   "source": [
    "using DFTK\n",
    "using AtomsBase\n",
    "using Unitful\n",
    "using UnitfulAtomic\n",
    "\n",
    "# Construct a system in the AtomsBase world\n",
    "a = 10.26u\"bohr\"  # Silicon lattice constant\n",
    "lattice = a / 2 * [[0, 1, 1.],  # Lattice as vector of vectors\n",
    "                   [1, 0, 1.],\n",
    "                   [1, 1, 0.]]\n",
    "atoms  = [:Si => ones(3)/8, :Si => -ones(3)/8]\n",
    "system = periodic_system(atoms, lattice; fractional=true)"
   ],
   "metadata": {},
   "execution_count": 1
  },
  {
   "cell_type": "markdown",
   "source": [
    "System is an AtomsBase-compatible system. To use it in DFTK,\n",
    "we attach pseudopotentials, construct a DFT model, discretise and solve:"
   ],
   "metadata": {}
  },
  {
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "n     Energy            log10(ΔE)   log10(Δρ)   Diag\n",
      "---   ---------------   ---------   ---------   ----\n",
      "  1   -7.921672534470                   -0.69    5.8\n",
      "  2   -7.926167862025       -2.35       -1.22    1.0\n",
      "  3   -7.926855247635       -3.16       -2.36    2.1\n",
      "  4   -7.926865039523       -5.01       -3.14    3.0\n",
      "  5   -7.926865071010       -7.50       -3.51    2.0\n",
      "  6   -7.926865085272       -7.85       -3.86    2.0\n",
      "  7   -7.926865092847       -8.12       -4.76    2.8\n"
     ]
    }
   ],
   "cell_type": "code",
   "source": [
    "system = attach_psp(system; family=\"hgh\", functional=\"lda\")\n",
    "\n",
    "model  = model_LDA(system; temperature=1e-3)\n",
    "basis  = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])\n",
    "scfres = self_consistent_field(basis, tol=1e-8);"
   ],
   "metadata": {},
   "execution_count": 2
  },
  {
   "cell_type": "markdown",
   "source": [
    "At any point we can also get back the DFTK model as an\n",
    "AtomsBase-compatible `AbstractSystem`:"
   ],
   "metadata": {}
  },
  {
   "outputs": [
    {
     "output_type": "execute_result",
     "data": {
      "text/plain": "FlexibleSystem(Si₂, AtomsBase.Periodic, box=[[0.0, 5.13, 5.13], [5.13, 0.0, 5.13], [5.13, 5.13, 0.0]]u\"a₀\")"
     },
     "metadata": {},
     "execution_count": 3
    }
   ],
   "cell_type": "code",
   "source": [
    "newsystem = atomic_system(model)"
   ],
   "metadata": {},
   "execution_count": 3
  }
 ],
 "nbformat_minor": 3,
 "metadata": {
  "language_info": {
   "file_extension": ".jl",
   "mimetype": "application/julia",
   "name": "julia",
   "version": "1.8.3"
  },
  "kernelspec": {
   "name": "julia-1.8",
   "display_name": "Julia 1.8.3",
   "language": "julia"
  }
 },
 "nbformat": 4
}