{
"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": [],
"cell_type": "code",
"source": [
"using DFTK\n",
"using AtomsBuilder"
],
"metadata": {},
"execution_count": 1
},
{
"cell_type": "markdown",
"source": [
"## Feeding an AtomsBase AbstractSystem to DFTK\n",
"\n",
"In this example we construct a bulk silicon system using the `bulk` function\n",
"from [AtomsBuilder](https://github.com/JuliaMolSim/AtomsBuilder.jl). This function\n",
"uses tabulated data to set up a reasonable starting geometry and lattice for bulk silicon."
],
"metadata": {}
},
{
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": "FlexibleSystem(Si₂, periodicity = TTT):\n cell_vectors : [ 0 2.715 2.715;\n 2.715 0 2.715;\n 2.715 2.715 0]u\"Å\"\n\n Atom(Si, [ 0, 0, 0]u\"Å\")\n Atom(Si, [ 1.3575, 1.3575, 1.3575]u\"Å\")\n"
},
"metadata": {},
"execution_count": 2
}
],
"cell_type": "code",
"source": [
"system = bulk(:Si)"
],
"metadata": {},
"execution_count": 2
},
{
"cell_type": "markdown",
"source": [
"By default the atoms of an `AbstractSystem` employ the bare Coulomb potential.\n",
"To employ pseudpotential models (which is almost always advisable for\n",
"plane-wave DFT) one employs the `pseudopotential` keyword argument in\n",
"model constructors such as `model_DFT`.\n",
"For example we can employ a `PseudoFamily` object\n",
"from the [PseudoPotentialData](https://github.com/JuliaMolSim/PseudoPotentialData.jl)\n",
"package. See its documentation for more information on the available\n",
"pseudopotential families and how to select them."
],
"metadata": {}
},
{
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": "Model(lda_x+lda_c_pw, 3D):\n lattice (in Bohr) : [0 , 5.13061 , 5.13061 ]\n [5.13061 , 0 , 5.13061 ]\n [5.13061 , 5.13061 , 0 ]\n unit cell volume : 270.11 Bohr³\n\n atoms : Si₂\n atom potentials : ElementPsp(Si, \"/home/runner/.julia/artifacts/326db5c901e2681584ec5c06fc17f6c96e516ff9/Si.upf\")\n ElementPsp(Si, \"/home/runner/.julia/artifacts/326db5c901e2681584ec5c06fc17f6c96e516ff9/Si.upf\")\n\n num. electrons : 8\n spin polarization : none\n temperature : 0.001 Ha\n smearing : DFTK.Smearing.FermiDirac()\n\n terms : Kinetic()\n AtomicLocal()\n AtomicNonlocal()\n Ewald(nothing)\n PspCorrection()\n Hartree()\n Xc(lda_x, lda_c_pw)\n Entropy()"
},
"metadata": {},
"execution_count": 3
}
],
"cell_type": "code",
"source": [
"using PseudoPotentialData # defines PseudoFamily\n",
"\n",
"pd_lda_family = PseudoFamily(\"dojo.nc.sr.lda.v0_4_1.standard.upf\")\n",
"model = model_DFT(system; functionals=LDA(), temperature=1e-3,\n",
" pseudopotentials=pd_lda_family)"
],
"metadata": {},
"execution_count": 3
},
{
"cell_type": "markdown",
"source": [
"Alternatively the `pseudopotentials` object also accepts a `Dict{Symbol,String}`,\n",
"which provides for each element symbol the filename or identifier\n",
"of the pseudopotential to be employed, e.g."
],
"metadata": {}
},
{
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": "Model(lda_x+lda_c_pw, 3D):\n lattice (in Bohr) : [0 , 5.13061 , 5.13061 ]\n [5.13061 , 0 , 5.13061 ]\n [5.13061 , 5.13061 , 0 ]\n unit cell volume : 270.11 Bohr³\n\n atoms : Si₂\n atom potentials : ElementPsp(Si, \"/home/runner/.julia/artifacts/966fd9cdcd7dbaba6dc2bf43ee50dd81e63e8837/Si.gth\")\n ElementPsp(Si, \"/home/runner/.julia/artifacts/966fd9cdcd7dbaba6dc2bf43ee50dd81e63e8837/Si.gth\")\n\n num. electrons : 8\n spin polarization : none\n temperature : 0.001 Ha\n smearing : DFTK.Smearing.FermiDirac()\n\n terms : Kinetic()\n AtomicLocal()\n AtomicNonlocal()\n Ewald(nothing)\n PspCorrection()\n Hartree()\n Xc(lda_x, lda_c_pw)\n Entropy()"
},
"metadata": {},
"execution_count": 4
}
],
"cell_type": "code",
"source": [
"path_to_pspfile = PseudoFamily(\"cp2k.nc.sr.lda.v0_1.semicore.gth\")[:Si]\n",
"model = model_DFT(system; functionals=LDA(), temperature=1e-3,\n",
" pseudopotentials=Dict(:Si => path_to_pspfile))"
],
"metadata": {},
"execution_count": 4
},
{
"cell_type": "markdown",
"source": [
"We can then discretise such a model and solve:"
],
"metadata": {}
},
{
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"n Energy log10(ΔE) log10(Δρ) Diag Δtime\n",
"--- --------------- --------- --------- ---- ------\n",
" 1 -7.921681503863 -0.69 5.5 839ms\n",
" 2 -7.926133575373 -2.35 -1.22 1.0 770ms\n",
" 3 -7.926833524972 -3.15 -2.37 2.0 152ms\n",
" 4 -7.926861274900 -4.56 -2.99 2.9 199ms\n",
" 5 -7.926861645407 -6.43 -3.38 2.2 162ms\n",
" 6 -7.926861670500 -7.60 -3.84 1.4 141ms\n",
" 7 -7.926861679389 -8.05 -4.17 1.8 146ms\n",
" 8 -7.926861681752 -8.63 -4.90 1.6 148ms\n",
" 9 -7.926861681834 -10.08 -5.00 2.2 160ms\n",
" 10 -7.926861681869 -10.46 -5.69 1.1 137ms\n",
" 11 -7.926861681872 -11.48 -6.12 2.2 162ms\n",
" 12 -7.926861681873 -12.59 -7.10 1.8 152ms\n",
" 13 -7.926861681873 -13.52 -7.41 2.9 202ms\n",
" 14 -7.926861681873 -14.75 -7.75 1.1 141ms\n",
" 15 -7.926861681873 + -Inf -8.16 1.6 196ms\n"
]
}
],
"cell_type": "code",
"source": [
"basis = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])\n",
"scfres = self_consistent_field(basis, tol=1e-8);"
],
"metadata": {},
"execution_count": 5
},
{
"cell_type": "markdown",
"source": [
"If we did not want to use\n",
"[AtomsBuilder](https://github.com/JuliaMolSim/AtomsBuilder.jl)\n",
"we could of course use any other package\n",
"which yields an AbstractSystem object. This includes:"
],
"metadata": {}
},
{
"cell_type": "markdown",
"source": [
"### Reading a system using AtomsIO\n",
"\n",
"Read a file using [AtomsIO](https://github.com/mfherbst/AtomsIO.jl),\n",
"which directly yields an AbstractSystem."
],
"metadata": {}
},
{
"outputs": [],
"cell_type": "code",
"source": [
"using AtomsIO\n",
"system = load_system(\"Si.extxyz\");"
],
"metadata": {},
"execution_count": 6
},
{
"cell_type": "markdown",
"source": [
"Run the LDA calculation:"
],
"metadata": {}
},
{
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"n Energy log10(ΔE) log10(Δρ) Diag Δtime\n",
"--- --------------- --------- --------- ---- ------\n",
" 1 -7.921730371012 -0.69 5.8 187ms\n",
" 2 -7.926131411206 -2.36 -1.22 1.0 133ms\n",
" 3 -7.926833365786 -3.15 -2.37 2.1 154ms\n",
" 4 -7.926861259195 -4.55 -3.00 3.1 241ms\n",
" 5 -7.926861647203 -6.41 -3.39 2.1 159ms\n",
" 6 -7.926861671123 -7.62 -3.84 1.4 139ms\n",
" 7 -7.926861679640 -8.07 -4.18 1.8 172ms\n",
" 8 -7.926861681772 -8.67 -4.90 1.4 140ms\n",
" 9 -7.926861681856 -10.08 -5.18 1.8 150ms\n",
" 10 -7.926861681871 -10.82 -5.84 1.8 148ms\n",
" 11 -7.926861681873 -11.74 -6.41 2.0 155ms\n",
" 12 -7.926861681873 -13.00 -7.52 1.8 155ms\n",
" 13 -7.926861681873 -14.15 -8.00 3.5 197ms\n",
" 14 -7.926861681873 + -14.75 -8.78 2.0 153ms\n"
]
}
],
"cell_type": "code",
"source": [
"pseudopotentials = PseudoFamily(\"cp2k.nc.sr.lda.v0_1.semicore.gth\")\n",
"model = model_DFT(system; pseudopotentials, functionals=LDA(), 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": 7
},
{
"cell_type": "markdown",
"source": [
"The same could be achieved using [ExtXYZ](https://github.com/libAtoms/ExtXYZ.jl)\n",
"by `system = Atoms(read_frame(\"Si.extxyz\"))`,\n",
"since the `ExtXYZ.Atoms` object is directly AtomsBase-compatible."
],
"metadata": {}
},
{
"cell_type": "markdown",
"source": [
"### Directly setting up a system in AtomsBase"
],
"metadata": {}
},
{
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"n Energy log10(ΔE) log10(Δρ) Diag Δtime\n",
"--- --------------- --------- --------- ---- ------\n",
" 1 -7.921728831917 -0.69 5.6 218ms\n",
" 2 -7.926138025114 -2.36 -1.22 1.0 143ms\n",
" 3 -7.926836807033 -3.16 -2.37 2.0 147ms\n",
" 4 -7.926864499287 -4.56 -2.99 3.0 195ms\n",
" 5 -7.926865060810 -6.25 -3.37 2.1 156ms\n",
" 6 -7.926865082027 -7.67 -3.84 1.2 128ms\n",
" 7 -7.926865089458 -8.13 -4.06 1.9 141ms\n"
]
}
],
"cell_type": "code",
"source": [
"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)\n",
"\n",
"# Now run the LDA calculation:\n",
"pseudopotentials = PseudoFamily(\"cp2k.nc.sr.lda.v0_1.semicore.gth\")\n",
"model = model_DFT(system; pseudopotentials, functionals=LDA(), temperature=1e-3)\n",
"basis = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])\n",
"scfres = self_consistent_field(basis, tol=1e-4);"
],
"metadata": {},
"execution_count": 8
},
{
"cell_type": "markdown",
"source": [
"## Obtaining an AbstractSystem from DFTK data"
],
"metadata": {}
},
{
"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, periodicity = TTT):\n cell_vectors : [ 0 5.13 5.13;\n 5.13 0 5.13;\n 5.13 5.13 0]u\"a₀\"\n\n Atom(Si, [ 1.2825, 1.2825, 1.2825]u\"a₀\")\n Atom(Si, [ -1.2825, -1.2825, -1.2825]u\"a₀\")\n"
},
"metadata": {},
"execution_count": 9
}
],
"cell_type": "code",
"source": [
"second_system = atomic_system(model)"
],
"metadata": {},
"execution_count": 9
},
{
"cell_type": "markdown",
"source": [
"Similarly DFTK offers a method to the `atomic_system` and `periodic_system` functions\n",
"(from AtomsBase), which enable a seamless conversion of the usual data structures for\n",
"setting up DFTK calculations into an `AbstractSystem`:"
],
"metadata": {}
},
{
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": "FlexibleSystem(Si₂, periodicity = TTT):\n cell_vectors : [ 0 5.13155 5.13155;\n 5.13155 0 5.13155;\n 5.13155 5.13155 0]u\"a₀\"\n\n Atom(Si, [ 1.28289, 1.28289, 1.28289]u\"a₀\")\n Atom(Si, [-1.28289, -1.28289, -1.28289]u\"a₀\")\n"
},
"metadata": {},
"execution_count": 10
}
],
"cell_type": "code",
"source": [
"lattice = 5.431u\"Å\" / 2 * [[0 1 1.];\n",
" [1 0 1.];\n",
" [1 1 0.]];\n",
"Si = ElementPsp(:Si, pseudopotentials)\n",
"atoms = [Si, Si]\n",
"positions = [ones(3)/8, -ones(3)/8]\n",
"\n",
"third_system = atomic_system(lattice, atoms, positions)"
],
"metadata": {},
"execution_count": 10
}
],
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"language_info": {
"file_extension": ".jl",
"mimetype": "application/julia",
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