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+
+
+
+ 20241009151249-936ad3d017b759e9132b271c7f89a4280a8c88f7
+ 20241009151249
+
+ JOSS Admin
+ admin@theoj.org
+
+ The Open Journal
+
+
+
+
+ Journal of Open Source Software
+ JOSS
+ 2475-9066
+
+ 10.21105/joss
+ https://joss.theoj.org
+
+
+
+
+ 10
+ 2024
+
+
+ 9
+
+ 102
+
+
+
+ Bodge: Python package for efficient tight-binding
+modeling of superconducting nanostructures
+
+
+
+ Jabir Ali
+ Ouassou
+ https://orcid.org/0000-0002-3725-0885
+
+
+
+ 10
+ 09
+ 2024
+
+
+ 7134
+
+
+ 10.21105/joss.07134
+
+
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
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+ 10.5281/zenodo.13839641
+
+
+ GitHub review issue
+ https://github.com/openjournals/joss-reviews/issues/7134
+
+
+
+ 10.21105/joss.07134
+ https://joss.theoj.org/papers/10.21105/joss.07134
+
+
+ https://joss.theoj.org/papers/10.21105/joss.07134.pdf
+
+
+
+
+
+ Numerical solutions to non-linear
+inhomogeneous problems in superconductivity
+ Benfenati
+ 2022
+ Benfenati, A. L. (2022). Numerical
+solutions to non-linear inhomogeneous problems in superconductivity [PhD
+thesis, KTH].
+https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-311403
+
+
+ Efficient numerical approach to inhomogeneous
+superconductivity: The Chebyshev–Bogoliubov–de Gennes
+method
+ Covaci
+ Physical Review Letters
+ 105
+ 10.1103/PhysRevLett.105.167006
+ 0031-9007
+ 2010
+ Covaci, L., Peeters, F. M., &
+Berciu, M. (2010). Efficient numerical approach to inhomogeneous
+superconductivity: The Chebyshev–Bogoliubov–de Gennes method. Physical
+Review Letters, 105, 167006.
+https://doi.org/10.1103/PhysRevLett.105.167006
+
+
+ Superconductivity of metals and
+alloys
+ de Gennes
+ 10.1201/9780429497032
+ 9780429497032
+ 1966
+ de Gennes, P. G. (1966).
+Superconductivity of metals and alloys.
+https://doi.org/10.1201/9780429497032
+
+
+ Efficient linear scaling algorithm for
+tight-binding molecular dynamics
+ Goedecker
+ Physical Review Letters
+ 73
+ 10.1103/PhysRevLett.73.122
+ 0031-9007
+ 1994
+ Goedecker, S., & Colombo, L.
+(1994). Efficient linear scaling algorithm for tight-binding molecular
+dynamics. Physical Review Letters, 73, 122–125.
+https://doi.org/10.1103/PhysRevLett.73.122
+
+
+ Kwant: A software package for quantum
+transport
+ Groth
+ New Journal of Physics
+ 16
+ 10.1088/1367-2630/16/6/063065
+ 2014
+ Groth, C. W., Wimmer, M., Akhmerov,
+A. R., & Waintal, X. (2014). Kwant: A software package for quantum
+transport. New Journal of Physics, 16, 063065.
+https://doi.org/10.1088/1367-2630/16/6/063065
+
+
+ Pybinding: A python package for tight-binding
+calculations
+ Moldovan
+ Zenodo
+ 10.5281/Zenodo.4010216
+ 2020
+ Moldovan, Dean, Anđelković, Miša,
+& Peeters, F. (2020). Pybinding: A python package for tight-binding
+calculations. Zenodo.
+https://doi.org/10.5281/Zenodo.4010216
+
+
+ N-independent localized Krylov–Bogoliubov-de
+Gennes method: Ultra-fast numerical approach to large-scale
+inhomogeneous superconductors
+ Nagai
+ Journal of the Physical Society of
+Japan
+ 89
+ 10.7566/JPSJ.89.074703
+ 0031-9015
+ 2020
+ Nagai, Y. (2020). N-independent
+localized Krylov–Bogoliubov-de Gennes method: Ultra-fast numerical
+approach to large-scale inhomogeneous superconductors. Journal of the
+Physical Society of Japan, 89, 074703.
+https://doi.org/10.7566/JPSJ.89.074703
+
+
+ Reduced-shifted conjugate-gradient method for
+a Green’s function: Efficient numerical approach in a nano-structured
+superconductor
+ Nagai
+ Journal of the Physical Society of
+Japan
+ 86
+ 10.7566/JPSJ.86.014708
+ 0031-9015
+ 2017
+ Nagai, Y., Shinohara, Y., Futamura,
+Y., & Sakurai, T. (2017). Reduced-shifted conjugate-gradient method
+for a Green’s function: Efficient numerical approach in a
+nano-structured superconductor. Journal of the Physical Society of
+Japan, 86, 014708.
+https://doi.org/10.7566/JPSJ.86.014708
+
+
+ DC Josephson effect in
+altermagnets
+ Ouassou
+ Physical Review Letters
+ 131
+ 10.1103/PhysRevLett.131.076003
+ 0031-9007
+ 2023
+ Ouassou, J. A., Brataas, A., &
+Linder, J. (2023). DC Josephson effect in altermagnets. Physical Review
+Letters, 131, 076003.
+https://doi.org/10.1103/PhysRevLett.131.076003
+
+
+ Electric control of superconducting
+transition through a spin-orbit coupled interface
+ Ouassou
+ Scientific Reports
+ 6
+ 10.1038/SRep29312
+ 2016
+ Ouassou, J. A., Bernardo, A. D.,
+Robinson, J. W. A., & Linder, J. (2016). Electric control of
+superconducting transition through a spin-orbit coupled interface.
+Scientific Reports, 6, 29312.
+https://doi.org/10.1038/SRep29312
+
+
+ Dzyaloshinskii–Moriya spin–spin interaction
+from mixed-parity superconductivity
+ Ouassou
+ 10.48550/arXiv.2407.07144
+ 2024
+ Ouassou, J. A., Yokoyama, T., &
+Linder, J. (2024). Dzyaloshinskii–Moriya spin–spin interaction from
+mixed-parity superconductivity.
+https://doi.org/10.48550/arXiv.2407.07144
+
+
+ Manipulating superconductivity in magnetic
+nanostructures in and out of equilibrium
+ Ouassou
+ 2019
+ Ouassou, J. A. (2019). Manipulating
+superconductivity in magnetic nanostructures in and out of equilibrium
+[PhD thesis, NTNU].
+https://pvv.org/~jabirali/academic/phd.pdf
+
+
+ RKKY interaction in triplet superconductors:
+Dzyaloshinskii–Moriya-type interaction mediated by spin-polarized Cooper
+pairs
+ Ouassou
+ Physical Review B
+ 109
+ 10.1103/PhysRevB.109.174506
+ 2469-9950
+ 2024
+ Ouassou, J. A., Yokoyama, T., &
+Linder, J. (2024). RKKY interaction in triplet superconductors:
+Dzyaloshinskii–Moriya-type interaction mediated by spin-polarized Cooper
+pairs. Physical Review B, 109, 174506.
+https://doi.org/10.1103/PhysRevB.109.174506
+
+
+ SciPy 1.0: Fundamental Algorithms for
+Scientific Computing in Python
+ Virtanen
+ Nature Methods
+ 17
+ 10.1038/S41592-019-0686-2
+ 2020
+ Virtanen, P., Gommers, R., Oliphant,
+T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson,
+P., Weckesser, W., Bright, J., van der Walt, S. J., Brett, M., Wilson,
+J., Millman, K. J., Mayorov, N., Nelson, A. R. J., Jones, E., Kern, R.,
+Larson, E., … SciPy 1.0 Contributors. (2020). SciPy 1.0: Fundamental
+Algorithms for Scientific Computing in Python. Nature Methods, 17,
+261–272.
+https://doi.org/10.1038/S41592-019-0686-2
+
+
+ The kernel polynomial method
+ Weiße
+ Reviews of Modern Physics
+ 78
+ 10.1103/RevModPhys.78.275
+ 2006
+ Weiße, A., Wellein, G., Alvermann,
+A., & Fehske, H. (2006). The kernel polynomial method. Reviews of
+Modern Physics, 78, 275–306.
+https://doi.org/10.1103/RevModPhys.78.275
+
+
+ Bogoliubov–de Gennes method and its
+applications
+ Zhu
+ 10.1007/978-3-319-31314-6
+ 9783319313122
+ 2016
+ Zhu, J.-X. (2016). Bogoliubov–de
+Gennes method and its applications.
+https://doi.org/10.1007/978-3-319-31314-6
+
+
+
+
+
+
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+
+
+
+
+
+
+
+Journal of Open Source Software
+JOSS
+
+2475-9066
+
+Open Journals
+
+
+
+7134
+10.21105/joss.07134
+
+Bodge: Python package for efficient tight-binding
+modeling of superconducting nanostructures
+
+
+
+https://orcid.org/0000-0002-3725-0885
+
+Ouassou
+Jabir Ali
+
+jabir.ali.ouassou@hvl.no
+
+
+
+
+
+Department of Computer Science, Electrical Engineering and
+Mathematical Sciences, Western Norway University of Applied Sciences,
+NO-5528 Haugesund, Norway
+
+
+
+
+Center for Quantum Spintronics, Department of Physics,
+Norwegian University of Science and Technology, NO-7491 Trondheim,
+Norway
+
+
+
+
+12
+7
+2024
+
+9
+102
+7134
+
+Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)
+2022
+The article authors
+
+Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)
+
+
+
+python
+numerical physics
+condensed matter physics
+tight-binding models
+superconductivity
+sparse matrices
+bdg equations
+
+
+
+
+
+ Summary
+
Bodge
+ is a Python package for constructing large-scale real-space
+ tight-binding models for calculations in condensed matter
+ physics. “Large-scale” means that it should remain performant even for
+ lattices with millions of atoms, and “real-space” means that the model
+ is formulated in terms of individual lattice sites and not in momentum
+ space, for example.
+
Although general tight-binding models can be constructed with this
+ package, the main focus is on the Bogoliubov–De Gennes (“BoDGe”)
+ Hamiltonian used to model superconductivity in the clean limit
+ (de
+ Gennes, 1966;
+ Zhu,
+ 2016). The package is designed to be easy to use, flexible, and
+ extensible—and very few lines of code are required to model
+ heterostructures containing, e.g., conventional and unconventional
+ superconductors, ferromagnets and antiferromagnets, altermagnetism,
+ and spin-orbit coupling.
+
In other words: If you want a lattice model for superconducting
+ nanostructures, and want something that is computationally efficient
+ yet easy to use, Bodge should be a good choice.
+
+
+ Statement of need
+
In condensed matter physics, a standard methodology for modeling
+ materials is the tight-binding model. In the context
+ of electronic systems (e.g., metals), the electrons in such a model
+ typically “live” at one atomic site, but from time to time “hop” over
+ to neighboring atoms. By including a spin structure as well in this
+ formalism—meaning that we keep track of what spins each electron has,
+ and whether the spins “flip” during various interactions that are
+ permitted on this lattice—we can model a wide variety of physical
+ phenomena including superconductivity and magnetism. Mathematically,
+ this is often expressed in the language of quantum field theory: We
+ define one operator
+
+ ciσ†
+ that “puts” an electron with spin
+
+ σ∈{↑,↓}
+ on an atomic site with some index
+
+ i,
+ and another operator
+
+ ciσ
+ that “removes” a corresponding electron. The Hamiltonian operator
+
+
+ ℋ
+ of the system is then constructed out of these electron operators—and
+ this can in turn be used to calculate, e.g., the ground-state energy,
+ electric currents, superconducting order parameters, and other
+ relevant material properties.
+
To do anything useful with that Hamiltonian on a
+ computer, however, you typically have to translate it to a
+ matrix form. This is where Bodge enters the picture:
+
+
+
It provides an easy-to-use Pythonic interface for constructing
+ the Hamiltonian of a tight-binding system. Particular focus has
+ been placed on making it easy to describe systems that include
+ various forms of superconductivity and magnetism, making it a
+ great choice for modeling, e.g., superconductivity in magnetic
+ heterostructures.
+
+
+
It scales well to large systems. For efficiency, it uses SciPy
+ sparse matrices internally
+ (Virtanen
+ et al., 2020), and it constructs large Hamiltonians in
+
+
+ 𝒪(N)
+ time and memory where
+
+ N
+ is the number of sites. According to
+ my
+ benchmarks, the performance is similar to
+ Kwant
+ (Groth
+ et al., 2014), which is the state of the art for numerical
+ condensed matter physics. The results can be returned in most
+ NumPy or SciPy matrix formats.
+
+
+
It is designed to be extensible. For instance, while Bodge
+ currently only implements square and cubic lattices (via the
+ CubicLattice class), it can be used to
+ construct Hamiltonians on triangular or hexagonal lattices if you
+ want: you just need to create your own subclass of the
+ Lattice base class and implement
+ two-to-three short iterators that describe how to iterate through
+ your lattice. (Specifically: the methods
+ .sites, .bonds, and
+ .edges need separate implementations per
+ Lattice type.)
+
+
+
Some convenience methods are provided to help you with the next
+ steps of your calculations: Extracting the local density of states
+ (LDOS), calculating the free energy, diagonalizing the
+ Hamiltonian, etc. (Some more advanced algorithms live on the
+ develop branch on GitHub, but have not yet
+ been assimilated into the official package.)
+
+
+
The code itself follows modern software development practices:
+ Full test coverage with continuous integration (via
+ pytest), fast runtime type checking (via
+ beartype), and PEP-8 compliance (via
+ black).
+
+
+
There are two main alternatives that arguably fill a similar niche
+ to Bodge: Kwant
+ (Groth
+ et al., 2014) and Pybinding
+ (Moldovan
+ et al., 2020). Compared to these packages, the main benefit of
+ Bodge is the focus on the BdG Hamiltonian in particular. For instance,
+ using Kwant, it is up to the user to declare that each lattice site
+ has four degrees of freedom (spin-up electrons, spin-down electrons,
+ spin-up holes, and spin-down holes), and to ensure that you construct
+ a Hamiltonian with the correct particle-hole symmetries. Bodge,
+ however, assumes that these are the only relevant
+ degrees of freedom, and enforces the relevant symmetries by default.
+ In practice, this means that Kwant can be used to study a broader
+ variety of physical systems, whereas Bodge can provide a friendlier
+ syntax for users who work specifically on superconducting systems.
+ Both packages support both NumPy arrays and SciPy sparse matrices as
+ output formats, and both provide similar performance in the limit of
+ large systems.
+
Sparse matrices, including, e.g., the Compressed Sparse
+ Row (CSR) format used below, have the advantage that they
+ only store the non-zero elements of a matrix. For a typical
+ tight-binding model with nearest-neighbor hopping terms, the
+ Hamiltonian matrix that describes a lattice with
+
+
+ N
+ atoms has
+
+ 𝒪(N2)
+ elements where only
+
+ 𝒪(N)
+ are non-zero. Thus, algorithms that leverage sparse matrices often
+ result in at least an
+
+ 𝒪(N)
+ reduction in CPU and RAM requirements, which becomes highly
+ significant for large systems. Even larger performance enhancements
+ can be obtained in some limits
+ (Nagai,
+ 2020;
+ Weiße
+ et al., 2006), although it depends on your system whether the
+ required approximations provide a good trade-off between accuracy and
+ speed. However, dense matrices (i.e., NumPy arrays)
+ allow for simpler solution algorithms based on, e.g., full matrix
+ diagonalization, and can become faster than sparse matrix algorithms
+ for small systems or when leveraging GPU acceleration. Notably, the
+ computational complexity of sparse matrix algorithms often come with a
+ large constant prefactor (e.g., the order of a Chebyshev matrix
+ expansion), which can actually result in worse performance for smaller
+ systems. For this reason, both sparse and dense matrices are fully
+ supported by Bodge, allowing the user to pick the most suitable matrix
+ format for the task at hand.
+
+
+ Examples and workflows
+
Introductory examples of how to use Bodge are provided in the
+ official
+ documentation. Examples of research problems that have been
+ studied using Bodge include superconductor/altermagnet
+ heterostructures
+ (Ouassou
+ et al., 2023) and RKKY interactions in unconventional
+ superconductors
+ (Ouassou
+ et al., 2024b,
+ 2024a).
+ These papers also describe some sparse matrix algorithms that can be
+ used together with Bodge, including Chebyshev expansion of the Fermi
+ matrix
+ (Benfenati,
+ 2022;
+ Goedecker
+ & Colombo, 1994;
+ Ouassou
+ et al., 2023;
+ Weiße
+ et al., 2006) and a quick way to calculate the local density of
+ states
+ (Nagai
+ et al., 2017;
+ Ouassou
+ et al., 2024b).
+
For a simple example of how this package can be used, consider a
+
+
+ 64a×64a
+ square lattice. Let’s assume that the whole system is a metal with
+ chemical potential
+
+ μ=1.5t,
+ where
+
+ t=1
+ is the hopping amplitude. Moreover, let’s assume that half the system
+ (
+
+ x<32a)
+ is a conventional
+
+ s-wave
+ superconductor with an order parameter
+
+ Δs=0.1t,
+ whereas the other half is a ferromagnet with exchange field
+
+
+ 𝐌=Mz𝐞z.
+ To describe the Hamiltonian corresponding to this system we can use
+ the following code:
+ from bodge import *
+
+# Tight-binding parameters
+t = 1
+μ = 1.5 * t
+Δs = 0.1 * t
+Mz = 0.5 * Δs
+
+# Construct the Hamiltonian
+lattice = CubicLattice((64, 64, 1))
+system = Hamiltonian(lattice)
+
+with system as (H, Δ):
+ for i, j in lattice.bonds():
+ H[i, j] = -t * σ0
+ for i in lattice.sites():
+ if i[0] < 32:
+ H[i, i] = -μ * σ0
+ Δ[i, i] = -Δs * jσ2
+ else:
+ H[i, i] = -μ * σ0 - Mz * σ3
+
Note the use of a context manager
+ (with-block) to provide an intuitive array
+ syntax for accessing the relevant parts of the Hamiltonian matrix,
+ while abstracting away the underlying sparse matrix details.
+ Afterwards, there are many different ways to use the resulting
+ object.
+
Some physical observables can be directly calculated using the
+ methods provided in Bodge. For instance, one can use the method
+ system.ldos(site, energies) to directly
+ calculate the local density of states at a given lattice site, which
+ can then be used to check for spectral features such as a
+ superconducting gap or a zero-energy
+ peak. There is also a method
+ system.free_energy(temperature) which
+ calculates the free energy of the system. By varying
+ parameters in the Hamiltonian (e.g., the orientation of a magnetic
+ field) and then minimizing this free energy, one can determine the
+ ground state of the system, for example.
+
Most calculations of interest, however, requires that the user
+ implements some code themselves. There are then two main approaches
+ one can take. The classic approach is matrix
+ diagonalization which uses dense matrices internally. Bodge
+ provides the method diagonalize for this
+ purpose:
+ E, v = system.diagonalize()
+
The results above contain the positive energies
+
+
+ En
+ and corresponding state vectors
+
+ 𝐯n
+ which satisfy the eigenvalue equation
+
+ 𝐇𝐯n=En𝐯n.
+ (Only positive eigenvalues are returned due to the “Nambu doubling” of
+ degrees of freedom in superconducting systems.) Once the eigenvalues
+ and eigenvectors have been obtained, the user can themselves calculate
+ physical properties of interest from these using equations from
+ standard textbooks on the “Bogoliubov–de Gennes” approach to modeling
+ superconductivity
+ (Zhu,
+ 2016). It is a future goal to incorporate more calculation
+ methods of this kind into the Bodge package itself. Support for matrix
+ diagonalization using GPUs via the CuPy package is also under
+ development.
+
Examples of physical observables that can be calculated from the
+ eigenvalues and eigenvectors include the superconducting order
+ parameter, electric currents, and spin currents. These can in turn be
+ used to calculate even more material properties. For instance, the
+ critical current of a Josephson junction is defined as the largest
+ electric current that can flow through it for any phase difference,
+ and the critical temperature of a bulk superconductor is defined as
+ the largest temperature at which the superconducting order parameter
+ remains non-zero. These observables can thus be determined via
+ numerical optimization of the electric current and superconducting
+ order parameter, respectively. For instance, the critical temperature
+ can be efficiently determined using a bisection method
+ (Ouassou
+ et al., 2016;
+ Ouassou,
+ 2019).
+
A modern alternative to matrix diagonalization is a series of
+ algorithms based on Chebyshev expansion of the Hamiltonian matrix
+ (Benfenati,
+ 2022;
+ Covaci
+ et al., 2010;
+ Nagai,
+ 2020;
+ Ouassou
+ et al., 2023;
+ Weiße
+ et al., 2006). These algorithms take advantage of the extreme
+ sparsity of the Hamiltonian matrix, and thus typically provide a
+ significant performance benefit in the limit of very large lattices.
+ One of the main design goals behind Bodge has been to make it trivial
+ to construct sparse representations of the Hamiltonian matrix for this
+ purpose, and it is therefore straight-forward to export the result as,
+ e.g., a CSR sparse matrix:
+ H = system.matrix(format="csr")
+
The user can then easily use the resulting matrix
+
+
+ 𝐇
+ to formulate their own sparse matrix algorithms of this kind. For
+ instance, arbitrary matrix functions can typically be evaluated as a
+ Chebyshev expansion
+
+ f(𝐇)=∑m=0M−1fmTm(𝐇),
+ where the Chebyshev moments
+
+ fm
+ of the function
+
+ f(⋅)
+ are computationally inexpensive to obtain, whereas the Chebyshev
+ matrix polynomials
+
+ Tm(⋅)
+ can be obtained via the recursion relation
+ (Weiße
+ et al., 2006)
+ 1$.} \end{cases}]]>
+ Tm(𝐇)={𝐇mif 0≤m≤1,2𝐇Tm−1(𝐇)−Tm−2(𝐇)if m>1.
+ The trick is then to find a suitable matrix function
+
+
+ f(𝐇)
+ to study your physical system. Using the “Kernel Polynomial Method”
+ (Weiße
+ et al., 2006), the order
+
+ M
+ of such a Chebyshev expansion can be decreased without serious
+ truncation errors.
+
+
+ Acknowledgements
+
I acknowledge very helpful discussions with my PostDoc supervisor
+ Prof. Jacob Linder when learning the BdG formalism, without which the
+ Bodge package would not exist today. I also thank Morten Amundsen,
+ Henning G. Hugdal, and Sol H. Jacobsen for useful discussions on
+ tight-binding modeling in general. Finally, I want to thank Mayeul
+ d’Avezac and Yue-Wen Fang for their constructive input during the
+ referee process, which has improved the Bodge software package and its
+ documentation.
+
This work was supported by the Research Council of Norway through
+ Grant No. 323766 and its Centres of Excellence funding scheme Grant
+ No. 262633 “QuSpin.” During the development of this package, some
+ numerical calculations were performed on resources provided by
+ Sigma2—the National Infrastructure for High Performance Computing and
+ Data Storage in Norway, Project No. NN9577K. The work presented in
+ this paper has also benefited from the Experimental Infrastructure for
+ Exploration of Exascale Computing (eX3), which is financially
+ supported by the Research Council of Norway under contract 270053.
+
+
+
+
+
+
+
+
+ BenfenatiAndrea Ludovico
+
+ Numerical solutions to non-linear inhomogeneous problems in superconductivity
+ KTH
+ Stockholm, Sweden
+ 2022
+ https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-311403
+
+
+
+
+
+ CovaciL.
+ PeetersF. M.
+ BerciuM.
+
+ Efficient numerical approach to inhomogeneous superconductivity: The Chebyshev–Bogoliubov–de Gennes method
+
+ 2010
+ 105
+ 0031-9007
+ 10.1103/PhysRevLett.105.167006
+ 167006
+
+
+
+
+
+
+ de GennesPierre Gilles
+
+
+ 1966
+ 9780429497032
+ 10.1201/9780429497032
+
+
+
+
+
+ GoedeckerS.
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