Merge pull request #3 from epolack/cell_to_supercell

Cell to supercell
LaurentVidal95 · Oct 20, 2022 · 40e81fd · 40e81fd
2 parents 1972d2f + 4529158
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.8
+current_version = 0.5.11
 commit = True
 tag = False
 

diff --git a/CITATION.bib b/CITATION.bib
@@ -1,6 +1,6 @@
 % Extended abstract describing DFTK along with a short summary of its features
 @article{DFTKjcon,
-  author = {Michael F. Herbst and Antoine Levitt and Eric Cancès},
+  author = {Herbst, Michael F. and Levitt, Antoine and Cancès, Eric},
   doi = {10.21105/jcon.00069},
   journal = {Proc. JuliaCon Conf.},
   title = {DFTK: A Julian approach for simulating electrons in solids},
@@ -9,13 +9,33 @@ @article{DFTKjcon
   year = {2021},
 }
 
+% Paper describing the calculation of response properties in DFTK.
+% Used for forward-diff derivatives, `solve_ΩplusK_split` and `apply_χ0` functions.
+@unpublished{ResponseCalculations,
+  author = {Cancès, Eric and Herbst, Michael F. and Kemlin, Gaspard and Levitt, Antoine and Stamm, Benjamin},
+  title = {Numerical Stability and Efficiency of Response Property Calculations in Density Functional Theory},
+  year = {Submitted},
+  note = {https://arxiv.org/abs/2210.04512},
+}
+
+% Paper describing the energy cutoff smearing method `BlowupCHV`
+@unpublished{BlowupCHV,
+  author = {Cancès, Eric and Hassan, Muhammad and Vidal, Laurent Vidal},
+  title = {Modified-Operator Method for the Calculation of Band Diagrams of Crystalline Materials},
+  year = {Submitted},
+  note = {https://hal.archives-ouvertes.fr/hal-03794000/},
+}
+
 % Paper describing the adaptive damping strategy implemented by
 % the scf_potential_mixing_adaptive function
-@unpublished{AdaptiveDamping,
+@article{AdaptiveDamping,
   author = {Herbst, Michael F. and Levitt, Antoine},
+  doi = {10.1016/j.jcp.2022.111127},
+  journal = {Journal of Computational Physics},
   title = {A robust and efficient line search for self-consistent field iterations},
-  year = {submitted},
-  note = {arXiv:2109.14018},
+  volume = {459},
+  pages = {111127},
+  year = {2022},
 }
 
 % Paper describing the HybridMixing, DielectricMixing and LdosMixing SCF preconditioners

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,27 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: 'DFTK: The Density-functional toolkit'
+message: Cite this paper whenever you use DFTK.
+type: software
+authors:
+  - email: [email protected]
+    given-names: Michael F.
+    family-names: Herbst
+    affiliation: RWTH Aachen University
+    orcid: 'https://orcid.org/0000-0003-0378-7921'
+  - family-names: Levitt
+    given-names: Antoine
+    email: [email protected]
+    affiliation: Inria Paris
+  - given-names: Eric
+    family-names: Cancès
+    email: [email protected]
+    affiliation: 'CERMICS, Ecole des Ponts'
+identifiers:
+  - type: doi
+    value: 10.21105/jcon.00069
+    description: Extended abstract describing the software
+url: 'https://dftk.org'
+license: MIT
diff --git a/Project.toml b/Project.toml
@@ -1,19 +1,19 @@
 name = "DFTK"
 uuid = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
 authors = ["Michael F. Herbst <[email protected]>", "Antoine Levitt <[email protected]>"]
-version = "0.5.8"
+version = "0.5.11"
 
 [deps]
 AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
-BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
 Brillouin = "23470ee3-d0df-4052-8b1a-8cbd6363e7f0"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DftFunctionals = "6bd331d2-b28d-4fd3-880e-1a1c7f37947f"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
 InteratomicPotentials = "a9efe35a-c65d-452d-b8a8-82646cd5cb04"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
@@ -48,21 +48,21 @@ spglib_jll = "ac4a9f1e-bdb2-5204-990c-47c8b2f70d4e"
 [compat]
 AbstractFFTs = "1"
 AtomsBase = "0.2.2"
-BlockArrays = "0.16.2"
-Brillouin = "0.5 - 0.5.8"  # Upper bound temporary until memory bug resolved.
+Brillouin = "0.5.4"
 ChainRulesCore = "1.15"
 Conda = "1"
 DftFunctionals = "0.2"
 FFTW = "1"
 ForwardDiff = "0.10"
+GPUArraysCore = "0.1"
 InteratomicPotentials = "0.2"
 Interpolations = "0.12, 0.13, 0.14"
 IterTools = "1"
 IterativeSolvers = "0.8, 0.9"
 Libxc = "0.3.9"
 LineSearches = "7"
 LinearMaps = "2, 3"
-MPI = "0.19"
+MPI = "0.19, 0.20"
 NLsolve = "4"
 Optim = "1"
 OrderedCollections = "1"
@@ -84,6 +84,7 @@ spglib_jll = "1.15"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 DoubleFloats = "497a8b3b-efae-58df-a0af-a86822472b78"
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
@@ -101,4 +102,4 @@ WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 wannier90_jll = "c5400fa0-8d08-52c2-913f-1e3f656c1ce9"
 
 [targets]
-test = ["Test", "Aqua", "DoubleFloats", "FiniteDiff", "FiniteDifferences", "GenericLinearAlgebra", "IntervalArithmetic", "Plots", "Random", "KrylovKit", "Logging", "JLD2", "WriteVTK", "wannier90_jll", "QuadGK", "ComponentArrays"]
+test = ["Test", "Aqua", "CUDA", "DoubleFloats", "FiniteDiff", "FiniteDifferences", "GenericLinearAlgebra", "IntervalArithmetic", "Plots", "Random", "KrylovKit", "Logging", "JLD2", "WriteVTK", "wannier90_jll", "QuadGK", "ComponentArrays"]
diff --git a/README.md b/README.md
@@ -4,16 +4,16 @@
 
 | **Documentation**                                                                 | **Build Status**                                |  **License**                     |
 |:--------------------------------------------------------------------------------- |:----------------------------------------------- |:-------------------------------- |
-| [![][docs-img]][docs-url] [![][ddocs-img]][ddocs-url] [![][slack-img]][slack-url] | [![][ci-img]][ci-url] [![][ccov-img]][ccov-url] | [![][license-img]][license-url]  |
+| [![][docs-img]][docs-url] [![][ddocs-img]][ddocs-url] [![][zulip-img]][zulip-url] | [![][ci-img]][ci-url] [![][ccov-img]][ccov-url] | [![][license-img]][license-url]  |
 
 [ddocs-img]: https://img.shields.io/badge/docs-dev-blue.svg
 [ddocs-url]: https://docs.dftk.org/dev
 
 [docs-img]: https://img.shields.io/badge/docs-stable-blue.svg
 [docs-url]: https://docs.dftk.org/stable
 
-[slack-img]: https://img.shields.io/badge/chat-on_slack-808493.svg?logo=slack
-[slack-url]: https://join.slack.com/t/juliamolsim/shared_invite/zt-tc060co0-HgiKApazzsQzBHDlQ58A7g
+[zulip-img]: https://img.shields.io/badge/chat-on_zulip-808493.svg?logo=zulip
+[zulip-url]: https://juliamolsim.zulipchat.com/#narrow/stream/332493-dftk
 
 [ci-img]: https://github.com/JuliaMolSim/DFTK.jl/workflows/CI/badge.svg?branch=master&event=push
 [ci-url]: https://github.com/JuliaMolSim/DFTK.jl/actions
@@ -76,4 +76,4 @@ on github. If you want to contribute but are unsure where to start, take a look
 at the list of issues tagged [good first issue](https://github.com/JuliaMolSim/DFTK.jl/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22)
 (relatively easy tasks suitable for newcomers) or [help wanted](https://github.com/JuliaMolSim/DFTK.jl/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22)
 (more sizeable but well-defined and isolated).
-Don't hesitate to ask for help, through github, email or the [JuliaMolSim slack][slack-url].
+Don't hesitate to ask for help, through github, email or the [JuliaMolSim zulip chat][zulip-url].
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,6 @@
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+Brillouin = "23470ee3-d0df-4052-8b1a-8cbd6363e7f0"
 DFTK = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"

diff --git a/docs/src/guide/tutorial.jl b/docs/src/guide/tutorial.jl
@@ -82,10 +82,10 @@ hcat(scfres.eigenvalues...)
 # k-point because there are 4 occupied states in the system (4 valence
 # electrons per silicon atom, two atoms per unit cell, and paired
 # spins), and the eigensolver gives itself some breathing room by
-# computing some extra states (see `n_ep_extra` argument to
-# `self_consistent_field`). There are only 8 k-points (instead of
-# 4x4x4) because symmetry has been used to reduce the amount of
-# computations to just the irreducible k-points (see
+# computing some extra states (see the `bands` argument to
+# `self_consistent_field` as well as the [`AdaptiveBands`](@ref) documentation).
+# There are only 8 k-points (instead of 4x4x4) because symmetry has been used to reduce the
+# amount of computations to just the irreducible k-points (see
 #md # [Crystal symmetries](@ref)
 #nb # [Crystal symmetries](https://docs.dftk.org/stable/developer/symmetries/)
 # for details).

diff --git a/docs/src/publications.md b/docs/src/publications.md
@@ -20,9 +20,20 @@ The current DFTK reference paper to cite is
 
 Additionally the following publications describe DFTK or one of its algorithms:
 
+- E. Cancès, M. F. Herbst, G. Kemlin, A. Levitt and B. Stamm.
+  [*Numerical stability and efficiency of response property calculations in density functional theory*](https://arxiv.org/abs/2210.04512)
+  (Submitted).
+  [ArXiv:2210.04512](https://arxiv.org/abs/2210.04512).
+  ([Supplementary material and computational scripts](https://github.com/gkemlin/response-calculations-metals)).
+
+- E. Cancès, M. Hassan and L. Vidal.
+  [*Modified-Operator Method for the Calculation of Band Diagrams of Crystalline Materials.*](https://hal.archives-ouvertes.fr/hal-03794000)
+  (Submitted).
+  [hal-03794000](https://hal.archives-ouvertes.fr/hal-03794000).
+
 - M. F. Herbst and A. Levitt.
   [*A robust and efficient line search for self-consistent field iterations*](https://arxiv.org/abs/2109.14018)
-  (Submitted).
+  Journal of Computational Physics, **459**, 111127 (2022).
   [ArXiv:2109.14018](https://arxiv.org/abs/2109.14018).
   ([Supplementary material and computational scripts](https://github.com/mfherbst/supporting-adaptive-damping/)).
 
@@ -41,12 +52,28 @@ Additionally the following publications describe DFTK or one of its algorithms:
 The following publications report research employing DFTK as a core component.
 Feel free to drop us a line if you want your work to be added here.
 
+- J. Cazalis.
+  [*Dirac cones for a mean-field model of graphene*](https://arxiv.org/abs/2207.09893)
+  (Submitted).
+  [ArXiv:2207.09893](https://arxiv.org/abs/2207.09893).
+  ([Computational script](https://github.com/JuliaMolSim/DFTK.jl/blob/f7fcc31c79436b2582ac1604d4ed8ac51a6fd3c8/examples/publications/2022_cazalis.jl)).
+
+- E. Cancès, L. Garrigue, D. Gontier.
+  [*A simple derivation of moiré-scale continuous models for twisted bilayer graphene*](https://arxiv.org/abs/2206.05685)
+  (Submitted).
+  [ArXiv:2206.05685](https://arxiv.org/abs/2206.05685).
+
 - E. Cancès, G. Dusson, G. Kemlin and A. Levitt.
   [*Practical error bounds for properties in plane-wave electronic structure calculations*](https://arxiv.org/abs/2111.01470)
   (Submitted).
   [ArXiv:2111.01470](https://arxiv.org/abs/2111.01470).
   ([Supplementary material and computational scripts](https://github.com/gkemlin/paper-forces-estimator)).
 
+- G. Dusson, I. Sigal and B. Stamm.
+  [*Analysis of the Feshbach-Schur method for the Fourier spectral discretizations of Schrödinger operators*](http://dx.doi.org/10.1090/mcom/3774)
+  Mathematics of Computation, **?**, ?? (2022).
+  [ArXiv:2008.10871](https://arxiv.org/abs/2008.10871).
+
 - E. Cancès, G. Kemlin and A. Levitt.
   [*Convergence analysis of direct minimization and self-consistent iterations*](https://doi.org/10.1137/20M1332864)
   SIAM Journal on Matrix Analysis and Applications, **42**, 243 (2021).

diff --git a/examples/cohen_bergstresser.jl b/examples/cohen_bergstresser.jl
@@ -18,12 +18,12 @@ lattice = Si.lattice_constant / 2 .* [[0 1 1.]; [1 0 1.]; [1 1 0.]];
 
 # Next we build the rather simple model and discretize it with moderate `Ecut`:
 model = Model(lattice, atoms, positions; terms=[Kinetic(), AtomicLocal()])
-basis = PlaneWaveBasis(model, Ecut=10.0, kgrid=(1, 1, 1));
+basis = PlaneWaveBasis(model, Ecut=10.0, kgrid=(2, 2, 2));
 
 # We diagonalise at the Gamma point to find a Fermi level …
 ham = Hamiltonian(basis)
 eigres = diagonalize_all_kblocks(DFTK.lobpcg_hyper, ham, 6)
-εF = DFTK.compute_occupation(basis, eigres.λ; occupation_threshold=0).εF
+εF = DFTK.compute_occupation(basis, eigres.λ).εF
 
 # … and compute and plot 8 bands:
 using Plots

diff --git a/examples/energy_cutoff_smearing.jl b/examples/energy_cutoff_smearing.jl
@@ -26,13 +26,9 @@
 using DFTK
 using Statistics
 
-a0 = 10.26 # Experimental lattice constant of silicon in bohr
+a0 = 10.26  # Experimental lattice constant of silicon in bohr
 a_list = range(a0 - 1/2, a0 + 1/2; length=20)
 
-Ecut    = 5         # very low Ecut to display big irregularities
-kgrid   = (2, 2, 2) # very sparse k-grid to fasten convergence
-n_bands = 8         # Standard number of bands for silicon
-
 function compute_ground_state_energy(a; Ecut, kgrid, kinetic_blowup, kwargs...)
     lattice = a / 2 * [[0 1 1.];
                        [1 0 1.];
@@ -42,12 +38,12 @@ function compute_ground_state_energy(a; Ecut, kgrid, kinetic_blowup, kwargs...)
     positions = [ones(3)/8, -ones(3)/8]
     model = model_PBE(lattice, atoms, positions; kinetic_blowup)
     basis = PlaneWaveBasis(model; Ecut, kgrid)
-    self_consistent_field(basis; kwargs...).energies.total
+    self_consistent_field(basis; callback=identity, kwargs...).energies.total
 end
 
-callback = info->nothing # set SCF to non verbose
-E0_naive = compute_ground_state_energy.(a_list; kinetic_blowup=BlowupIdentity(),
-                                        Ecut, kgrid, n_bands, callback);
+Ecut  = 5          # Very low Ecut to display big irregularities
+kgrid = (2, 2, 2)  # Very sparse k-grid to speed up convergence
+E0_naive = compute_ground_state_energy.(a_list; kinetic_blowup=BlowupIdentity(), Ecut, kgrid);
 
 # To be compared with the same computation for a high `Ecut=100`. The naive approximation
 # of the energy is shifted for the legibility of the plot.
@@ -74,8 +70,7 @@ plot!(p, a_list, E0_ref, label="Ecut=100", color=2)
 # that is mathematically ensured to provide ``C^2`` regularity of the energy bands.
 
 # Let us lauch the computation again with the modified kinetic term.
-E0_modified = compute_ground_state_energy.(a_list; kinetic_blowup=BlowupCHV(),
-                                           Ecut, kgrid, n_bands, callback, );
+E0_modified = compute_ground_state_energy.(a_list; kinetic_blowup=BlowupCHV(), Ecut, kgrid,);
 
 # !!! note "Abinit energy cutoff smearing option"
 #     For the sake of completeness, DFTK also provides the blow-up function `BlowupAbinit`
@@ -93,8 +88,7 @@ E0_modified = compute_ground_state_energy.(a_list; kinetic_blowup=BlowupCHV(),
 estimate_a0(E0_values) = a_list[findmin(E0_values)[2]]
 a0_naive, a0_ref, a0_modified = estimate_a0.([E0_naive, E0_ref, E0_modified])
 
-shift = mean(abs.(E0_modified .- E0_ref))  # again, shift for legibility of the plot
-
+shift = mean(abs.(E0_modified .- E0_ref))  # Shift for legibility of the plot
 plot!(p, a_list, E0_modified .- shift, label="Ecut=5 + BlowupCHV", color=3)
 vline!(p, [a0], label="experimental a0", linestyle=:dash, linecolor=:black)
 vline!(p, [a0_naive], label="a0 Ecut=5", linestyle=:dash, color=1)

diff --git a/examples/graphene.jl b/examples/graphene.jl
@@ -32,27 +32,7 @@ model = model_PBE(lattice, atoms, positions; temperature)
 basis = PlaneWaveBasis(model; Ecut, kgrid)
 scfres = self_consistent_field(basis)
 
-## Choose the points of the band diagram, in reduced coordinates (in the (b1,b2) basis)
-Γ  = [0, 0, 0]
-K  = [ 1, 1, 0]/3
-Kp = [-1, 2, 0]/3
-M  = (K + Kp)/2
-kpath_coords = [Γ, K, M, Γ]
-kpath_names  = ["Γ", "K", "M", "Γ"]
-
-## Build the path manually for now
-kline_density = 20
-function build_path(k1, k2)
-    target_Δk = 1/kline_density  # the actual Δk is |k2-k1|/npt
-    npt = ceil(Int, norm(model.recip_lattice * (k2-k1)) / target_Δk)
-    [k1 + t * (k2-k1) for t in range(0, 1, length=npt)]
-end
-kcoords = []
-for i = 1:length(kpath_coords)-1
-    append!(kcoords, build_path(kpath_coords[i], kpath_coords[i+1]))
-end
-klabels = Dict(zip(kpath_names, kpath_coords))
-
-## Plot the bands
-band_data = compute_bands(basis, kcoords; scfres.ρ)
-DFTK.plot_band_data(band_data; scfres.εF, klabels)
+## Construct 2D path through Brillouin zone
+sgnum = 13  # Graphene space group number
+kpath = irrfbz_path(model; dim=2, sgnum)
+plot_bandstructure(scfres, kpath; kline_density=20)
diff --git a/examples/publications/2022_cazalis.jl b/examples/publications/2022_cazalis.jl
@@ -1,5 +1,5 @@
 # Model of graphene confined to 2 spatial dimensions studied
-# in the paper by Cazalis (arxiv, 2022, TODO add ref)
+# in the paper by Cazalis (arxiv, 2022, https://arxiv.org/abs/2207.09893)
 # The pure 3D Coulomb 1/|x| interaction is used, without pseudopotential.
 
 using DFTK
@@ -59,30 +59,9 @@ basis = PlaneWaveBasis(model; Ecut, kgrid)
 ## Run SCF
 scfres = self_consistent_field(basis, tol=1e-10)
 
-## Choose the points of the band diagram, in reduced coordinates (in the (b1,b2) basis)
-Γ  = [0, 0, 0]
-K  = [ 1, 1, 0]/3
-Kp = [-1, 2, 0]/3
-M  = (K + Kp)/2
-kpath_coords = [Γ, K, M, Γ]
-kpath_names  = ["Γ", "K", "M", "Γ"]
-
-## Build the path
-kline_density = 20
-function build_path(k1, k2)
-    target_Δk = 1/kline_density  # the actual Δk is |k2-k1|/npt
-    npt = ceil(Int, norm(model.recip_lattice * (k2-k1)) / target_Δk)
-    [k1 + t * (k2-k1) for t in range(0, 1, length=npt)]
-end
-kcoords = []
-for i = 1:length(kpath_coords)-1
-    append!(kcoords, build_path(kpath_coords[i], kpath_coords[i+1]))
-end
-klabels = Dict(kpath_names[i] => kpath_coords[i] for i=1:length(kpath_coords))
-
-## Plot the bands
-band_data = compute_bands(basis, kcoords; n_bands=5, scfres.ρ)
-p = DFTK.plot_band_data(band_data; klabels, markersize=nothing)
+## Plot bands
+sgnum = 13  # Graphene space group number
+p = plot_bandstructure(scfres, irrfbz_path(model; sgnum); n_bands=5)
 Plots.hline!(p, [scfres.εF], label="", color="black")
-Plots.ylims!(p, -Inf,Inf)
+Plots.ylims!(p, (-Inf, Inf))
 p
diff --git a/examples/supercells.jl b/examples/supercells.jl
@@ -84,7 +84,7 @@ self_consistent_field(aluminium_setup(2); is_converged);
 
 #-
 
-self_consistent_field(aluminium_setup(4); is_converged, n_bands=30);
+self_consistent_field(aluminium_setup(4); is_converged);
 
 # When switching off explicitly the `LdosMixing`, by selecting `mixing=SimpleMixing()`,
 # the performance of number of required SCF steps starts to increase as we increase
@@ -94,7 +94,7 @@ self_consistent_field(aluminium_setup(1); is_converged, mixing=SimpleMixing());
 
 #-
 
-self_consistent_field(aluminium_setup(4); is_converged, mixing=SimpleMixing(), n_bands=30);
+self_consistent_field(aluminium_setup(4); is_converged, mixing=SimpleMixing());
 
 # For completion let us note that the more traditional `mixing=KerkerMixing()` 
 # approach would also help in this particular setting to obtain a constant