GeometryOptimization: minimize_energy! doesn't return the relaxed result of a lattice relaxation #1066
Comments
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Hi @thomsen59 thanks for reporting
I don't think that's the root cause here. It looks the error is from symmetrising the forces it computes. This looks very much like a bug. I see you extxyz file and you setup the calculator as: using AtomsIO # Use Julia-only IO parsers
system = load_system("geo2.extxyz")
using DFTK
using PseudoPotentialData
pseudopotentials = PseudoFamily("dojo.nc.sr.pbe.v0_4_1.standard.upf")
calc = DFTKCalculator(;
model_kwargs = (; functionals=PBE(), pseudopotentials),
basis_kwargs = (; kgrid=[2, 2, 3], Ecut=30),
)But I cannot see your geometry optimisation invocation. Can you post that, too, for reference ? |
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using DFTK using GeometryOptimization |
I loaded a particular lattice structure generated with ASE in extxyz format for GeO_2 (rutile). Then I tried to relax w/ GeometryOptimization. minimize_energy! ran a few loop-steps and the quit with
ERROR: ArgumentError: invalid index: nothing of type Nothing
perhaps it's got to do with 'miniter=2' when the structure is already relaxed?
versioninfo()
Julia Version 1.11.3
Commit d63adeda50d (2025-01-21 19:42 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: macOS (arm64-apple-darwin24.0.0)
CPU: 8 × Apple M2
WORD_SIZE: 64
LLVM: libLLVM-16.0.6 (ORCJIT, apple-m2)
Threads: 2 default, 0 interactive, 1 GC (on 4 virtual cores)
Environment:
LD_LIBRARY_PATH = /opt/homebrew/Cellar/libxc/7.0.0/lib
JULIA_EDITOR = code
JULIA_NUM_THREADS = 2
Program:
cd("/Users/thomsen/Documents/ct/_nach_P/julia/QM/rutile")
using Pkg; Pkg.gc
Pkg.activate(@DIR)
Pkg.instantiate(); Pkg.precompile()
using AtomsIO # Use Julia-only IO parsers
system = load_system("geo2.extxyz")
using DFTK
using PseudoPotentialData
pseudopotentials = PseudoFamily("dojo.nc.sr.pbe.v0_4_1.standard.upf")
calc = DFTKCalculator(;
model_kwargs = (; functionals=PBE(), pseudopotentials), # model_DFT keyword arguments
basis_kwargs = (; kgrid=[2, 2, 3], Ecut=30) # PlaneWaveBasis keyword arguments
)
model = model_DFT(system;
system:
6
Lattice="4.48609 0.0 0.0 0.0 4.48609 0.0 0.0 0.0 2.91186" Properties=species:S:1:pos:R:3:spacegroup_kinds:I:1 spacegroup="P 42/m n m" unit_cell=conventional pbc="T T T"
Ge 0.00000000 0.00000000 0.00000000 0
Ge 2.24304500 2.24304500 1.45593000 0
O 1.39068790 1.39068790 0.00000000 1
O 3.09540210 3.09540210 0.00000000 1
O 0.85235710 3.63373290 1.45593000 1
O 3.63373290 0.85235710 1.45593000 1
Output:
Activating project at
~/Documents/ct/_nach_P/julia/QM/rutile┌ Warning: Negative ρcore detected: -3.3604553205713266e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.4576296213 -0.28 0.80 6.3 10.0s
2 -244.3423400565 + -0.94 -0.18 0.80 3.7 5.74s
3 -244.7613250451 -0.38 -1.26 0.80 4.3 3.78s
4 -244.7617630308 -3.36 -1.98 0.80 1.2 1.64s
5 -244.7619099002 -3.83 -2.54 0.80 2.5 1.61s
6 -244.7619176983 -5.11 -2.71 0.80 2.2 1.60s
7 -244.7619198134 -5.67 -3.25 0.80 1.0 1.05s
8 -244.7619199842 -6.77 -3.32 0.80 2.3 1.70s
9 -244.7619201390 -6.81 -3.90 0.80 1.0 976ms
10 -244.7619201677 -7.54 -4.23 0.80 2.0 1.70s
11 -244.7619201698 -8.69 -4.62 0.80 1.0 1.02s
12 -244.7619201706 -9.09 -5.30 0.80 2.0 1.29s
13 -244.7619201706 -10.26 -5.35 0.80 2.0 1.48s
14 -244.7619201707 -10.86 -5.93 0.80 1.0 1.25s
15 -244.7619201707 -11.61 -6.47 0.80 3.0 1.38s
16 -244.7619201707 + -13.07 -6.79 0.80 2.0 1.56s
17 -244.7619201707 -12.59 -7.02 0.80 1.3 1.32s
18 -244.7619201707 + -13.25 -6.95 0.80 1.0 999ms
19 -244.7619201707 + -12.94 -7.14 0.80 1.0 987ms
20 -244.7619201707 -12.85 -8.49 0.80 1.0 1.25s
┌ Warning: Negative ρcore detected: -3.3604553205713266e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.7619201707 -8.63 0.80 1.0 2.03s
2 -244.7619201707 + -12.59 -8.75 0.80 1.0 1.07s
Geometry optimisation convergence (in atomic units)
┌─────┬─────────────────┬───────────┬────────────┬────────┐
│ n │ Energy │ log10(ΔE) │ max(Force) │ Δtime │
├─────┼─────────────────┼───────────┼────────────┼────────┤
│ 0 │ -244.7619201707 │ │ 0.222255 │ 63.4s │
└─────┴─────────────────┴───────────┴────────────┴────────┘
┌ Warning: Negative ρcore detected: -3.315597813538548e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.5373423838 -0.75 0.80 4.2 2.59s
2 -244.5500588879 -1.90 -1.47 0.80 1.0 2.12s
3 -244.5523112907 -2.65 -1.72 0.80 2.7 3.09s
4 -244.5518414556 + -3.33 -2.09 0.80 1.2 1.57s
5 -244.5519064618 -4.19 -2.61 0.80 1.0 1.37s
6 -244.5516643299 + -3.62 -2.81 0.80 2.0 2.35s
7 -244.5516729617 -5.06 -3.81 0.80 1.0 1.21s
8 -244.5516581321 + -4.83 -3.31 0.80 3.2 2.11s
9 -244.5516508194 + -5.14 -3.91 0.80 2.0 1.45s
10 -244.5516492958 + -5.82 -4.39 0.80 1.7 1.40s
11 -244.5516502289 -6.03 -4.79 0.80 1.2 1.01s
12 -244.5516505020 -6.56 -5.09 0.80 1.8 1.11s
13 -244.5516505000 + -8.69 -5.39 0.80 1.5 1.08s
14 -244.5516505757 -7.12 -5.86 0.80 2.0 1.56s
15 -244.5516505324 + -7.36 -6.16 0.80 1.8 1.16s
16 -244.5516505075 + -7.60 -6.88 0.80 1.7 1.05s
17 -244.5516505052 + -8.64 -7.12 0.80 2.2 1.46s
18 -244.5516505035 + -8.78 -7.64 0.80 1.2 1.32s
19 -244.5516505040 -9.31 -8.22 0.80 2.2 1.14s
20 -244.5516505041 -10.06 -8.57 0.80 2.5 1.39s
┌ Warning: Negative ρcore detected: -3.357364227037798e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.7466544874 -0.80 0.80 4.2 1.91s
2 -244.7579236597 -1.95 -1.51 0.80 1.0 986ms
3 -244.7597712273 -2.73 -1.79 0.80 2.3 1.31s
4 -244.7598933906 -3.91 -2.25 0.80 1.2 1.32s
5 -244.7599318113 -4.42 -2.70 0.80 2.2 1.85s
6 -244.7599519933 -4.70 -3.07 0.80 2.0 1.47s
7 -244.7599534891 -5.83 -3.55 0.80 1.7 1.36s
8 -244.7599536499 -6.79 -3.90 0.80 1.2 1.31s
9 -244.7599537712 -6.92 -4.98 0.80 2.0 1.25s
10 -244.7599538664 -7.02 -4.78 0.80 3.2 1.79s
11 -244.7599538663 + -10.24 -5.88 0.80 1.8 1.23s
12 -244.7599538692 -8.54 -6.27 0.80 3.0 1.89s
13 -244.7599538698 -9.22 -6.92 0.80 1.8 1.46s
14 -244.7599538699 -9.94 -7.07 0.80 1.8 1.28s
15 -244.7599538699 + -11.14 -8.10 0.80 1.0 1.03s
16 -244.7599538699 -11.27 -7.67 0.80 3.2 2.12s
17 -244.7599538699 -11.48 -8.00 0.80 1.7 1.43s
18 -244.7599538699 -11.99 -8.99 0.80 1.8 1.75s
┌ Warning: Negative ρcore detected: -3.359458083895236e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.7613841321 -2.05 0.80 1.0 1.80s
2 -244.7616248420 -3.62 -2.88 0.80 1.0 1.46s
3 -244.7617301400 -3.98 -2.95 0.80 3.5 2.80s
4 -244.7617302213 -7.09 -3.22 0.80 1.0 1.46s
5 -244.7617302936 -7.14 -3.94 0.80 1.0 1.85s
6 -244.7617305072 -6.67 -4.16 0.80 2.0 2.12s
7 -244.7617305346 -7.56 -4.80 0.80 1.0 1.35s
8 -244.7617305616 -7.57 -4.89 0.80 2.2 1.86s
9 -244.7617305629 -8.89 -5.30 0.80 1.0 1.15s
10 -244.7617305637 -9.11 -5.74 0.80 2.0 2.15s
11 -244.7617305641 -9.39 -6.11 0.80 1.2 1.92s
12 -244.7617305644 -9.56 -6.46 0.80 1.7 1.16s
13 -244.7617305645 -10.10 -7.42 0.80 1.8 1.23s
14 -244.7617305645 -10.23 -7.88 0.80 2.8 1.89s
15 -244.7617305645 -11.40 -7.87 0.80 1.7 1.18s
16 -244.7617305645 -12.94 -8.15 0.80 1.0 1.06s
17 -244.7617305645 -12.08 -8.31 0.80 2.0 2.03s
18 -244.7617305645 -12.25 -8.77 0.80 1.0 1.45s
┌ Warning: Negative ρcore detected: -3.360026398991296e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.7618612451 -2.60 0.80 1.0 1.41s
2 -244.7618833816 -4.65 -3.43 0.80 1.0 1.77s
3 -244.7618948160 -4.94 -3.50 0.80 3.5 4.10s
4 -244.7618948139 + -8.68 -3.77 0.80 1.0 1.46s
5 -244.7618948220 -8.09 -4.50 0.80 1.0 1.44s
6 -244.7618948483 -7.58 -4.71 0.80 2.0 2.15s
7 -244.7618948514 -8.50 -5.43 0.80 1.0 1.69s
8 -244.7618948547 -8.49 -5.44 0.80 2.3 2.02s
9 -244.7618948548 -9.92 -5.84 0.80 1.0 1.39s
10 -244.7618948548 -10.17 -6.28 0.80 2.0 1.61s
11 -244.7618948549 -10.38 -6.62 0.80 1.0 1.50s
12 -244.7618948549 -10.55 -7.04 0.80 1.7 1.30s
13 -244.7618948549 -10.97 -7.79 0.80 1.8 1.30s
14 -244.7618948549 -11.29 -7.84 0.80 2.2 1.41s
15 -244.7618948549 -12.40 -8.62 0.80 1.2 1.34s
┌ Warning: Negative ρcore detected: -3.3602512794195806e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.7619131870 -2.99 0.80 1.0 799ms
2 -244.7619170666 -5.41 -3.82 0.80 1.0 926ms
3 -244.7619191977 -5.67 -3.89 0.80 3.8 2.30s
4 -244.7619191975 + -9.69 -4.16 0.80 1.0 1.05s
5 -244.7619191992 -8.77 -4.86 0.80 1.0 1.01s
6 -244.7619192043 -8.29 -5.10 0.80 2.0 1.42s
7 -244.7619192049 -9.28 -5.94 0.80 1.0 1.36s
8 -244.7619192054 -9.23 -5.84 0.80 2.7 1.62s
9 -244.7619192055 -10.99 -6.20 0.80 1.0 1.08s
10 -244.7619192055 -11.50 -6.63 0.80 2.0 1.24s
11 -244.7619192055 -11.50 -6.99 0.80 1.0 2.98s
12 -244.7619192055 -11.40 -7.71 0.80 2.0 1.95s
13 -244.7619192055 -11.86 -7.94 0.80 2.8 2.35s
14 -244.7619192055 -12.37 -7.95 0.80 2.0 2.01s
15 -244.7619192055 -12.70 -8.35 0.80 1.0 1.80s
16 -244.7619192055 -12.77 -8.70 0.80 1.7 1.58s
┌ Warning: Negative ρcore detected: -3.360353977627203e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.7619209182 -3.33 0.80 1.0 1.14s
2 -244.7619217712 -6.07 -4.15 0.80 1.0 1.75s
3 -244.7619222529 -6.32 -4.22 0.80 3.8 3.82s
4 -244.7619222529 + -10.36 -4.50 0.80 1.0 1.38s
5 -244.7619222532 -9.43 -5.20 0.80 1.0 1.37s
6 -244.7619222544 -8.94 -5.44 0.80 2.0 1.88s
7 -244.7619222545 -9.92 -6.25 0.80 1.0 1.08s
8 -244.7619222547 -9.85 -6.17 0.80 2.5 1.52s
9 -244.7619222547 -11.71 -6.55 0.80 1.0 982ms
10 -244.7619222547 -11.98 -6.98 0.80 2.0 1.46s
11 -244.7619222547 -12.04 -7.31 0.80 1.0 1.02s
12 -244.7619222547 -12.13 -7.96 0.80 2.0 1.12s
13 -244.7619222547 -12.94 -8.43 0.80 2.7 1.31s
14 -244.7619222547 -12.47 -8.18 0.80 2.0 1.67s
15 -244.7619222547 + -Inf -8.95 0.80 2.0 1.25s
┌ Warning: Negative ρcore detected: -3.360353977627203e-5
└ @ DFTK ~/.julia/packages/DFTK/fpkCG/src/terms/xc.jl:39
n Energy log10(ΔE) log10(Δρ) α Diag Δtime
1 -244.7619222547 -9.54 0.80 1.0 778ms
2 -244.7619222547 -13.55 -10.18 0.80 1.0 1.15s
ERROR: ArgumentError: invalid index: nothing of type Nothing
Stacktrace:
[1] to_index(i::Nothing)
@ Base ./indices.jl:315
[2] to_index(A::Vector{Int64}, i::Nothing)
@ Base ./indices.jl:292
[3] to_indices
@ ./indices.jl:368 [inlined]
[4] to_indices
@ ./indices.jl:360 [inlined]
[5] getindex
@ ./abstractarray.jl:1312 [inlined]
[6] symmetrize_forces(model::Model{…}, forces::Vector{…}; symmetries::Vector{…})
@ DFTK ~/.julia/packages/DFTK/fpkCG/src/symmetry.jl:367
[7] symmetrize_forces
@ ~/.julia/packages/DFTK/fpkCG/src/symmetry.jl:355 [inlined]
[8] symmetrize_forces
@ ~/.julia/packages/DFTK/fpkCG/src/symmetry.jl:373 [inlined]
[9] compute_forces(::DFTK.TermAtomicNonlocal, basis::PlaneWaveBasis{…}, ψ::Vector{…}, occupation::Vector{…}; kwargs::@kwargs{…})
@ DFTK ./none:0
[10] compute_forces
@ ./none:0 [inlined]
[11] (::DFTK.var"#1026#1027"{@kwargs{…}, PlaneWaveBasis{…}, Vector{…}, Vector{…}})(term::DFTK.TermAtomicNonlocal)
@ DFTK ./none:0
[12] iterate
@ ./generator.jl:48 [inlined]
[13] collect_to!(dest::Vector{Union{…}}, itr::Base.Generator{Vector{…}, DFTK.var"#1026#1027"{…}}, offs::Int64, st::Int64)
@ Base ./array.jl:849
[14] collect_to!(dest::Vector{Nothing}, itr::Base.Generator{Vector{…}, DFTK.var"#1026#1027"{…}}, offs::Int64, st::Int64)
@ Base ./array.jl:857
[15] collect_to_with_first!(dest::Vector{…}, v1::Nothing, itr::Base.Generator{…}, st::Int64)
@ Base ./array.jl:827
[16] collect(itr::Base.Generator{Vector{Any}, DFTK.var"#1026#1027"{@kwargs{…}, PlaneWaveBasis{…}, Vector{…}, Vector{…}}})
@ Base ./array.jl:801
[17] compute_forces(basis::PlaneWaveBasis{…}, ψ::Vector{…}, occupation::Vector{…}; kwargs::@kwargs{…})
@ DFTK ./none:0
[18] compute_forces
@ ./none:0 [inlined]
[19] compute_forces_cart(basis::PlaneWaveBasis{…}, ψ::Vector{…}, occupation::Vector{…}; kwargs::@kwargs{…})
@ DFTK ~/.julia/packages/DFTK/fpkCG/src/postprocess/forces.jl:23
[20] compute_forces_cart
@ ~/.julia/packages/DFTK/fpkCG/src/postprocess/forces.jl:22 [inlined]
[21] compute_forces_cart(scfres::@NamedTuple{…})
@ DFTK ~/.julia/packages/DFTK/fpkCG/src/postprocess/forces.jl:31
[22] calculate(::AtomsCalculators.Forces, system::FlexibleSystem{…}, calc::DFTKCalculator{…}, ps::@NamedTuple{}, st::@NamedTuple{…}; kwargs::@kwargs{})
@ DFTK ~/.julia/packages/DFTK/fpkCG/src/external/DFTKCalculator.jl:141
[23] calculate(::AtomsCalculators.Forces, system::FlexibleSystem{…}, calc::DFTKCalculator{…}, ps::@NamedTuple{}, st::@NamedTuple{…})
@ DFTK ~/.julia/packages/DFTK/fpkCG/src/external/DFTKCalculator.jl:138
[24] (::GeometryOptimization.var"#13#16"{…})(G::Vector{…}, x::Vector{…}, ps::@NamedTuple{})
@ GeometryOptimization ~/.julia/packages/GeometryOptimization/A4i1q/src/optimization.jl:61
[25] (::OptimizationBase.var"#63#70"{…})(::Vector{…}, ::Vector{…})
@ OptimizationBase ~/.julia/packages/OptimizationBase/KIIy3/src/function.jl:142
[26] (::OptimizationOptimJL.var"#10#16"{OptimizationBase.OptimizationCache{…}})(G::Vector{Float64}, θ::Vector{Float64})
@ OptimizationOptimJL ~/.julia/packages/OptimizationOptimJL/hDX5k/src/OptimizationOptimJL.jl:193
[27] gradient!!(obj::NLSolversBase.TwiceDifferentiable{Float64, Vector{…}, Matrix{…}, Vector{…}}, x::Vector{Float64})
@ NLSolversBase ~/.julia/packages/NLSolversBase/kavn7/src/interface.jl:63
[28] value_gradient!(obj::NLSolversBase.TwiceDifferentiable{Float64, Vector{…}, Matrix{…}, Vector{…}}, x::Vector{Float64})
@ NLSolversBase ~/.julia/packages/NLSolversBase/kavn7/src/interface.jl:73
[29] update_g!(d::NLSolversBase.TwiceDifferentiable{…}, state::Optim.LBFGSState{…}, method::Optim.LBFGS{…})
@ Optim ~/.julia/packages/Optim/HvjCd/src/multivariate/optimize/optimize.jl:4
[30] optimize(d::NLSolversBase.TwiceDifferentiable{…}, initial_x::Vector{…}, method::Optim.LBFGS{…}, options::Optim.Options{…}, state::Optim.LBFGSState{…})
@ Optim ~/.julia/packages/Optim/HvjCd/src/multivariate/optimize/optimize.jl:59
[31] optimize(d::NLSolversBase.TwiceDifferentiable{…}, initial_x::Vector{…}, method::Optim.LBFGS{…}, options::Optim.Options{…})
@ Optim ~/.julia/packages/Optim/HvjCd/src/multivariate/optimize/optimize.jl:36
[32] __solve(cache::OptimizationBase.OptimizationCache{…})
@ OptimizationOptimJL ~/.julia/packages/OptimizationOptimJL/hDX5k/src/OptimizationOptimJL.jl:224
[33] solve!
@ ~/.julia/packages/SciMLBase/YTOjh/src/solve.jl:187 [inlined]
[34] #solve#725
@ ~/.julia/packages/SciMLBase/YTOjh/src/solve.jl:95 [inlined]
[35] _minimize_energy!(system::ExtXYZ.Atoms{…}, calculator::DFTKCalculator{…}, solver::GeometryOptimization.Autoselect; maxiters::Int64, maxtime::Int64, tol_energy::Unitful.Quantity{…}, tol_forces::Float64, tol_virial::Unitful.Quantity{…}, maxstep::Unitful.Quantity{…}, verbosity::Int64, callback::DFTKGeometryOptimizationExt.var"#4#6"{…}, kwargs::@kwargs{})
@ GeometryOptimization ~/.julia/packages/GeometryOptimization/A4i1q/src/optimization.jl:156
[36] minimize_energy!(system::ExtXYZ.Atoms{…}, calc::DFTKCalculator{…}, solver::GeometryOptimization.Autoselect; autoadjust_calculator::Bool, tol_energy::Unitful.Quantity{…}, tol_forces::Float64, tol_virial::Unitful.Quantity{…}, verbosity::Int64, callback::GeoOptDefaultCallback, kwargs::@kwargs{})
@ DFTKGeometryOptimizationExt ~/.julia/packages/DFTK/fpkCG/ext/DFTKGeometryOptimizationExt.jl:56
[37] top-level scope
@ ~/Documents/ct/_nach_P/julia/QM/rutile/geo2_relaxation _sent.jl:25
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