Merge pull request #622 from bangerth/dft-fe

Add the DFT-FE papers.

Author: marcfehling

publications-2019.bib

@@ -850,6 +850,19 @@ @Article{2019:ghesmati.bangerth.ea:residual-based
   publisher = {Walter de Gruyter {GmbH}}
 }
 
+@Article{2019:ghosh.ma.ea:all-electron,
+  author  = {Ghosh, Krishnendu and Ma, He and Gavini, Vikram and Galli, Giulia},
+  title   = {All-electron density functional calculations for electron and nuclear spin interactions in molecules and solids},
+  journal = {Physical Review Materials},
+  year    = 2019,
+  volume  = 3,
+  number  = 4,
+  month   = apr,
+  issn    = {2475-9953},
+  doi     = {10.1103/physrevmaterials.3.043801},
+  publisher = {American Physical Society (APS)}
+}
+
 @Article{2019:giuliani:blacknufft,
   author  = {Nicola Giuliani},
   title   = {{BlackNUFFT}: Modular customizable black box hybrid parallelization of type 3 {NUFFT} in 3D},
@@ -1208,6 +1221,19 @@ @PhDThesis{2019:jonathan-perry-hout:geodynamic-origin-of-the-columbia-river-floo
   url     = {http://hdl.handle.net/1794/24526}
 }
 
+@Article{2019:kanungo.zimmerman.ea:exact,
+  author  = {Kanungo, Bikash and Zimmerman, Paul M. and Gavini, Vikram},
+  title   = {Exact exchange-correlation potentials from ground-state electron densities},
+  journal = {Nature Communications},
+  year    = 2019,
+  volume  = 10,
+  number  = 1,
+  month   = oct,
+  issn    = {2041-1723},
+  doi     = {10.1038/s41467-019-12467-0},
+  publisher = {Springer Science and Business Media LLC}
+}
+
 @InProceedings{2019:kauffman.george.ea:overset,
   author  = {Justin A. Kauffman and William L. George and Jonathan S. Pitt},
   title   = {An Overset Mesh Framework for an Isentropic {ALE} Navier-Stokes {HDG} Formulation},

publications-2020.bib

@@ -2249,4 +2249,18 @@ @TechReport{2020:zheng.lammers.ea:engineered
   publisher = {Office of Scientific and Technical Information ({OSTI})}
 }
 
+@Article{2020:zhuravel.huang.ea:backbone,
+  author  = {Zhuravel, Roman and Huang, Haichao and Polycarpou, Georgia and Polydorides, Savvas and Motamarri, Phani and Katrivas, Liat and Rotem, Dvir and Sperling, Joseph and Zotti, Linda A. and Kotlyar, Alexander B. and Cuevas, Juan Carlos and Gavini, Vikram and Skourtis, Spiros S. and Porath, Danny},
+  title   = {Backbone charge transport in double-stranded DNA},
+  journal = {Nature Nanotechnology},
+  year    = 2020,
+  volume  = 15,
+  number  = 10,
+  pages   = {836--840},
+  month   = aug,
+  issn    = {1748-3395},
+  doi     = {10.1038/s41565-020-0741-2},
+  publisher = {Springer Science and Business Media LLC}
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}

publications-2021.bib

@@ -860,6 +860,19 @@ @InCollection{2021:gerken:dynamic
   url     = {https://link.springer.com/chapter/10.1007/978-3-030-57784-1_2}
 }
 
+@Article{2021:ghosh.ma.ea:spin-spin,
+  author  = {Ghosh, Krishnendu and Ma, He and Onizhuk, Mykyta and Gavini, Vikram and Galli, Giulia},
+  title   = {Spin-spin interactions in defects in solids from mixed all-electron and pseudopotential first-principles calculations},
+  journal = {npj Computational Materials},
+  year    = 2021,
+  volume  = 7,
+  number  = 1,
+  month   = jul,
+  issn    = {2057-3960},
+  doi     = {10.1038/s41524-021-00590-w},
+  publisher = {Springer Science and Business Media LLC}
+}
+
 @Article{2021:giani.grubisic.ea:smoothed-adaptive,
   author  = {Stefano Giani and Luka Grubi{\v{s}}i{\'{c}} and Luca Heltai and Ornela Mulita},
   title   = {Smoothed-Adaptive Perturbed Inverse Iteration for Elliptic Eigenvalue Problems},
@@ -1534,6 +1547,19 @@ @Article{2021:li.lipton.ea:lorentz
   doi     = {10.1098/rspa.2021.0609}
 }
 
+@Article{2021:lin.motamarri.ea:tensor-structured,
+  author  = {Lin, Chih-Chuen and Motamarri, Phani and Gavini, Vikram},
+  title   = {Tensor-structured algorithm for reduced-order scaling large-scale Kohn-Sham density functional theory calculations},
+  journal = {npj Computational Materials},
+  year    = 2021,
+  volume  = 7,
+  number  = 1,
+  month   = apr,
+  issn    = {2057-3960},
+  doi     = {10.1038/s41524-021-00517-5},
+  publisher = {Springer Science and Business Media LLC}
+}
+
 @Article{2021:liu.moller.ea:balancing,
   author  = {Jie Liu and Matthias M\"{o}ller and Henk M. Schuttelaars},
   title   = {Balancing truncation and round-off errors in {FEM}: One-dimensional analysis},
@@ -1980,6 +2006,19 @@ @MastersThesis{2021:roth:proper
   url     = {https://julianroth.org/res/Master_Thesis_Julian_Roth.pdf}
 }
 
+@Article{2021:rufus.kanungo.ea:fast,
+  author  = {Rufus, Nelson D. and Kanungo, Bikash and Gavini, Vikram},
+  title   = {Fast and robust all-electron density functional theory calculations in solids using orthogonalized enriched finite elements},
+  journal = {Physical Review B},
+  year    = 2021,
+  volume  = 104,
+  number  = 8,
+  month   = aug,
+  issn    = {2469-9969},
+  doi     = {10.1103/physrevb.104.085112},
+  publisher = {American Physical Society (APS)}
+}
+
 @Article{2021:russ.waisman:novel,
   author  = {Jonathan B. Russ and Haim Waisman},
   title   = {A novel elastoplastic topology optimization formulation for enhanced failure resistance via local ductile failure constraints and linear buckling analysis},
@@ -2309,6 +2348,19 @@ @Article{2021:vassaux.gopalakrishnan.ea:accelerating
   publisher = {Wiley}
 }
 
+@Article{2021:vaughn.gavini.ea:treecode-accelerated,
+  author  = {Vaughn, Nathan and Gavini, Vikram and Krasny, Robert},
+  title   = {Treecode-accelerated Green iteration for Kohn-Sham density functional theory},
+  journal = {Journal of Computational Physics},
+  year    = 2021,
+  volume  = 430,
+  pages   = 110101,
+  month   = apr,
+  issn    = {0021-9991},
+  doi     = {10.1016/j.jcp.2020.110101},
+  publisher = {Elsevier BV}
+}
+
 @Article{2021:veszelka.queisser.ea:impact,
   author  = {Veszelka, Z. and Queisser, O. and Gontscharow, M. and Wetzel, T. and D{\"o}rfler, W.},
   title   = {Impact of Numerical Methods in Thermal Modeling of {Li}-Ion Batteries on Temperature Distribution and Computation Time},

publications-2022.bib

@@ -665,6 +665,20 @@ @InProceedings{2022:dang:study
   url     = {https://onepetro.org/ISRMARMS/proceedings-abstract/ARMS1222/All-ARMS1222/515488}
 }
 
+@Article{2022:das.motamarri.ea:dft-fe,
+  author  = {Das, Sambit and Motamarri, Phani and Subramanian, Vishal and Rogers, David M. and Gavini, Vikram},
+  title   = {DFT-FE 1.0: A massively parallel hybrid CPU-GPU density functional theory code using finite-element discretization},
+  journal = {Computer Physics Communications},
+  year    = 2022,
+  volume  = 280,
+  pages   = 108473,
+  month   = nov,
+  issn    = {0010-4655},
+  url     = {http://dx.doi.org/10.1016/j.cpc.2022.108473},
+  doi     = {10.1016/j.cpc.2022.108473},
+  publisher = {Elsevier BV}
+}
+
 @Article{2022:dasika.vaghani.ea:constrained,
   author  = {Dasika, Sunder and Vaghani, Dipak and Shukla, Ratnesh K.},
   title   = {Constrained least-squares based adaptive-order finite-volume {WENO} scheme for the simulation of viscous compressible flows on unstructured grids},
@@ -977,6 +991,19 @@ @Article{2022:fumagalli.vitullo.ea:image-based
   publisher = {Frontiers}
 }
 
+@Article{2022:gao.liao.ea:electronic,
+  author  = {Gao, Yifan and Liao, Jiabao and Wang, Heyan and Wu, Yi and Li, Yilian and Wang, Kun and Ma, Chunlan and Gong, Shijing and Wang, Tianxing and Dong, Xiao and Jiao, Zhaoyong and An, Yipeng},
+  title   = {Electronic Transport Properties and Nanodevice Designs for Monolayer MoSi2P4},
+  journal = {Physical Review Applied},
+  year    = 2022,
+  volume  = 18,
+  number  = 3,
+  month   = sep,
+  issn    = {2331-7019},
+  doi     = {10.1103/physrevapplied.18.034033},
+  publisher = {American Physical Society (APS)}
+}
+
 @Article{2022:giambiagi.tassara.ea:crustal,
   author  = {Giambiagi, Laura and Tassara, Andr{\'e}s and Echaurren, Andr{\'e}s and Julve, Joaqu{\'\i}n and Quiroga, Rodrigo and Barrionuevo, Mat{\'\i}as and Liu, Sibiao and Echeverr{\'\i}a, I{\~n}igo and Mard{\'o}nez, Diego and Suriano, Julieta and others},
   title   = {Crustal anatomy and evolution of a subduction-related orogenic system: Insights from the Southern Central Andes (22-35{\textdegree}S)},
@@ -2593,6 +2620,20 @@ @Article{2022:xu.zhang.ea:comparison
   publisher = {American Physical Society ({APS})}
 }
 
+@Article{2022:yao.das.ea:modulating,
+  author  = {Yao, Lulu and Das, Sambit and Liu, Xin and Wu, Kai and Cheng, Yonghong and Gavini, Vikram and Xiao, Bing},
+  title   = {Modulating the microscopic lattice distortions through the Al-rich layers for boosting the ferroelectricity in Al:HfO2 nanofilms},
+  journal = {Journal of Physics D: Applied Physics},
+  year    = 2022,
+  volume  = 55,
+  number  = 45,
+  pages   = 455501,
+  month   = sep,
+  issn    = {1361-6463},
+  doi     = {10.1088/1361-6463/ac8f55},
+  publisher = {IOP Publishing}
+}
+
 @Article{2022:yin.li.ea:experiments,
   author  = {Yin, Peiran and Li, Rui and Yin, Chengjiang and Xu, Xiangyu and Bian, Xiang and Xie, Han and Duan, Chang-Kui and Huang, Pu and He, Jian-hua and Du, Jiangfeng},
   title   = {Experiments with levitated force sensor challenge theories of dark energy},

publications-2023.bib

@@ -509,6 +509,32 @@ @Article{2023:dannberg.chotalia.ea:how
   preprint = {https://www.researchsquare.com/article/rs-2949347/v1}
 }
 
+@Article{2023:das.gavini:accelerating,
+  author  = {Das, Sambit and Gavini, Vikram},
+  title   = {Accelerating self-consistent field iterations in Kohn-Sham density functional theory using a low-rank approximation of the dielectric matrix},
+  journal = {Physical Review B},
+  year    = 2023,
+  volume  = 107,
+  number  = 12,
+  month   = mar,
+  issn    = {2469-9969},
+  doi     = {10.1103/physrevb.107.125133},
+  publisher = {American Physical Society (APS)}
+}
+
+@InProceedings{2023:das.kanungo.ea:large-scale,
+  author  = {Das, Sambit and Kanungo, Bikash and Subramanian, Vishal and Panigrahi, Gourab and Motamarri, Phani and Rogers, David and Zimmerman, Paul and Gavini, Vikram},
+  title   = {Large-Scale Materials Modeling at Quantum Accuracy: Ab Initio Simulations of Quasicrystals and Interacting Extended Defects in Metallic Alloys},
+  booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
+  year    = 2023,
+  series  = {SC '23},
+  pages   = {1--12},
+  month   = nov,
+  publisher = {ACM},
+  doi     = {10.1145/3581784.3627037},
+  collection = {SC '23}
+}
+
 @Article{2023:daunais.barbeau.ea:extensive,
   author  = {Carole-Anne Daunais and Lucka Barbeau and Bruno Blais},
   title   = {An extensive study of shear thinning flow around a spherical particle for power-law and {C}arreau fluids},
@@ -688,6 +714,20 @@ @Article{2023:fuest.heydari.ea:global
   preprint = {https://arxiv.org/abs/2205.08168}
 }
 
+@Article{2023:gavini.baroni.ea:roadmap,
+  author  = {Gavini, Vikram and Baroni, Stefano and Blum, Volker and Bowler, David R and Buccheri, Alexander and Chelikowsky, James R and Das, Sambit and Dawson, William and Delugas, Pietro and Dogan, Mehmet and Draxl, Claudia and Galli, Giulia and Genovese, Luigi and Giannozzi, Paolo and Giantomassi, Matteo and Gonze, Xavier and Govoni, Marco and Gygi, Fran{\c c}ois and Gulans, Andris and Herbert, John M and Kokott, Sebastian and K{\"u}hne, Thomas D and Liou, Kai-Hsin and Miyazaki, Tsuyoshi and Motamarri, Phani and Nakata, Ayako and Pask, John E and Plessl, Christian and Ratcliff, Laura E and Richard, Ryan M and Rossi, Mariana and Schade, Robert and Scheffler, Matthias and Sch{\"u}tt, Ole and Suryanarayana, Phanish and Torrent, Marc and Truflandier, Lionel and Windus, Theresa L and Xu, Qimen and Yu, Victor W-Z and Perez, D},
+  title   = {Roadmap on electronic structure codes in the exascale era},
+  journal = {Modelling and Simulation in Materials Science and Engineering},
+  year    = 2023,
+  volume  = 31,
+  number  = 6,
+  pages   = 063301,
+  month   = aug,
+  issn    = {1361-651X},
+  doi     = {10.1088/1361-651x/acdf06},
+  publisher = {IOP Publishing}
+}
+
 @Article{2023:gea.mancilla.ea:overriding,
   author  = {Gea, Pedro J. and Mancilla, Flor de Lis and Negredo, Ana M. and Hunen, Jeroen van},
   title   = {Overriding plate thickness as a controlling factor for trench retreat rates in narrow subduction zones},
@@ -1106,6 +1146,19 @@ @Article{2023:kosin.beuchler.ea:new
   publisher = {Elsevier {BV}}
 }
 
+@Article{2023:kumar.ludhwani.ea:effect,
+  author  = {Kumar, Pranav and Ludhwani, Mohit M. and Das, Sambit and Gavini, Vikram and Kanjarla, Anand and Adlakha, Ilaksh},
+  title   = {Effect of hydrogen on plasticity of $\alpha$-Fe: A multi-scale assessment},
+  journal = {International Journal of Plasticity},
+  year    = 2023,
+  volume  = 165,
+  pages   = 103613,
+  month   = jun,
+  issn    = {0749-6419},
+  doi     = {10.1016/j.ijplas.2023.103613},
+  publisher = {Elsevier BV}
+}
+
 @InProceedings{2023:kundu.banerjee:effect,
   author  = {Animesh Kundu and Atanu Banerjee},
   title   = {Effect of Thermo-Mechanical Coupling and Large Deformation on the Response of SMA Structures},
@@ -1636,6 +1689,20 @@ @Article{2023:rajaonarison.stamps.ea:geodynamic
   eprint  = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2022JB025800}
 }
 
+@Article{2023:ramakrishnan.nori.ea:chemical,
+  author  = {Ramakrishnan, Kartick and Nori, Sai Krishna Kishore and Lee, Seung-Cheol and Das, Gour P. and Bhattacharjee, Satadeep and Motamarri, Phani},
+  title   = {Chemical Bonding in Large Systems Using Projected Population Analysis from Real-Space Density Functional Theory Calculations},
+  journal = {Journal of Chemical Theory and Computation},
+  year    = 2023,
+  volume  = 19,
+  number  = 13,
+  pages   = {4216--4231},
+  month   = jun,
+  issn    = {1549-9626},
+  doi     = {10.1021/acs.jctc.3c00114},
+  publisher = {American Chemical Society (ACS)}
+}
+
 @MastersThesis{2023:rich:limits,
   author  = {Rich, Jonathan},
   title   = {Limits of tectonic reactivation on Mars using Earth analogue analysis and numerical modeling},

publications-2024.bib

@@ -1338,6 +1338,17 @@ @Misc{2024:meggendorfer.kanschat.ea:monolithic
   copyright = {Creative Commons Attribution 4.0 International}
 }
 
+@Article{2024:menon.das.ea:atomistic,
+  author  = {Menon, Vaidehi and Das, Sambit and Gavini, Vikram and Qi, Liang},
+  title   = {Atomistic Simulations and Machine Learning of Solute Grain Boundary Segregation in Mg Alloys at Finite Temperatures},
+  journal = {Acta Materialia},
+  year    = 2024,
+  volume  = 264,
+  pages   = 119515,
+  doi     = {10.2139/ssrn.4546828},
+  publisher = {Elsevier BV}
+}
+
 @Article{2024:mishra.carrara.ea:multiscale,
   author  = {Mishra, A. and Carrara, P. and Marfia, S. and Sacco, E. and De Lorenzis, L.},
   title   = {Multiscale enhanced non-uniform transformation field analysis},
@@ -1839,6 +1850,19 @@ @Article{2024:shi.cai.ea:robust
   preprint = {https://arxiv.org/abs/2408.09692}
 }
 
+@Article{2024:shojaei.holber.ea:bridging,
+  author  = {Shojaei, M. Faghih and Holber, J. and Das, S. and Teichert, G.H. and Mueller, T. and Hung, L. and Gavini, V. and Garikipati, K.},
+  title   = {Bridging scales with Machine Learning: From first principles statistical mechanics to continuum phase field computations to study order-disorder transitions in LixCoO2},
+  journal = {Journal of the Mechanics and Physics of Solids},
+  year    = 2024,
+  volume  = 190,
+  pages   = 105726,
+  month   = sep,
+  issn    = {0022-5096},
+  doi     = {10.1016/j.jmps.2024.105726},
+  publisher = {Elsevier BV}
+}
+
 @Article{2024:sinigaglia.braghin.ea:optimal,
   author  = {Sinigaglia, Carlo and Braghin, Francesco and Serra, Mattia},
   title   = {Optimal Control of Short-Time Attractors in Active Nematics},
@@ -1877,6 +1901,20 @@ @Article{2024:stankiewicz.dev.ea:towards
   publisher = {Springer Science and Business Media LLC}
 }
 
+@Article{2024:subramanian.das.ea:tucker,
+  author  = {Subramanian, Vishal and Das, Sambit and Gavini, Vikram},
+  title   = {Tucker Tensor Approach for Accelerating Fock Exchange Computations in a Real-Space Finite-Element Discretization of Generalized Kohn-Sham Density Functional Theory},
+  journal = {Journal of Chemical Theory and Computation},
+  year    = 2024,
+  volume  = 20,
+  number  = 9,
+  pages   = {3566--3579},
+  month   = apr,
+  issn    = {1549-9626},
+  doi     = {10.1021/acs.jctc.4c00019},
+  publisher = {American Chemical Society (ACS)}
+}
+
 @Article{2024:sun.fei.ea:intermediate,
   author  = {Sun, Yuan and Fei, Fan and Wong, Louis Ngai Yuen and Choo, Jinhyun},
   title   = {Intermediate Principal Stress Effects on the 3D Cracking Behavior of Flawed Rocks Under True Triaxial Compression},