diff --git a/other/materials_designer/specific_examples/Introduction.ipynb b/other/materials_designer/specific_examples/Introduction.ipynb index db05278bb..08fdbdb11 100644 --- a/other/materials_designer/specific_examples/Introduction.ipynb +++ b/other/materials_designer/specific_examples/Introduction.ipynb @@ -50,21 +50,21 @@ "| `X-2D-PAS` | Passivated Surface | [Silicon Surface Passivation](passivation_surface_silicon.ipynb) | *To be added* | [[21]](#ref21) |\n", "| `X-1D-PAS` | Passivated Edge | [Si Nanowire Edge Passivation](passivation_edge_nanowire_silicon.ipynb) | *To be added* | [[22]](#ref22) |\n", "| `X-0D-PAS` | Passivated Edge | *To be added* | — | — |\n", - "| `X-0D-CUT` | Slab Cutout | [Custom Cutout in Etched Silicon](custom_cutout_etched_silicon.ipynb) | *To be added* | — |\n", + "| `X-0D-CUT` | Slab Cutout | [Custom Cutout in Etched Silicon](custom_cutout_etched_silicon.ipynb) | *To be added* | [[25]](#ref25) |\n", "\n", "## References\n", "\n", "[1] Eglitis, R. I., & Vanderbilt, D. (2008). First-principles calculations of atomic and electronic structure of SrTiO₃ (001) and (011) surfaces. *Physical Review B*, 77(19), 195408. https://doi.org/10.1103/PhysRevB.77.195408\n", "\n", - "[2] Larsen, A. H., et al. (2011). Structure optimization of supported gold clusters. *Physical Review B*, 84(24), 245429. https://doi.org/10.1103/PhysRevB.84.245429\n", + "[2] Larsen, A. H., et al. (2011). Electronic shell structure and chemisorption on gold nanoparticles. *Physical Review B*, 84(24), 245429. https://doi.org/10.1103/PhysRevB.84.245429\n", "\n", "[3] Muller, D. A., et al. (1999). The electronic structure at the atomic scale of ultrathin gate oxides. *Nature*, 399(6738), 758-761. https://doi.org/10.1038/21602\n", "\n", - "[4] Jung, J., et al. (2015). Moiré band model and band gaps of graphene on hexagonal boron nitride. *Nature Communications*, 6, 6308. https://doi.org/10.1038/ncomms7308\n", + "[4] Jung, J., et al. (2015). Origin of band gaps in graphene on hexagonal boron nitride. *Nature Communications*, 6, 6308. https://doi.org/10.1038/ncomms7308\n", "\n", "[5] Kang, Y.-J., Kang, J., & Chang, K. J. (2008). Electronic structure of graphene and doping effect on SiO₂. Physical Review B, 78(11), 115404. https://doi.org/10.1103/PhysRevB.78.115404\n", "\n", - "[6] Shan, T. R., et al. (2011). Molecular dynamics study of the adhesion of Cu/SiO₂ interfaces using a variable-charge interatomic potential. *Physical Review B*, 83(11), 115327. https://doi.org/10.1103/PhysRevB.83.115327\n", + "[6] Shan, T.-R., et al. (2011). Molecular dynamics study of the adhesion of Cu/SiO₂ interfaces using a variable-charge interatomic potential. *Physical Review B*, 83(11), 115327. https://doi.org/10.1103/PhysRevB.83.115327\n", "\n", "[7] Dahal, A., & Batzill, M. (2014). Graphene–nickel interfaces: a review. *Nanoscale*, 6(5), 2548-2562. https://doi.org/10.1039/c3nr05279f\n", "\n", @@ -78,19 +78,19 @@ "\n", "[12] Zou, X., et al. (2015). Grain boundary properties of elemental two-dimensional materials. *Nano Letters*, 15(5), 3495-3500. https://doi.org/10.1021/acs.nanolett.5b01852\n", "\n", - "[13] Frolov, T., et al. (2013). Structural phase transformations in metallic grain boundaries. *Nature Communications*, 4, 2919. https://doi.org/10.1038/ncomms2919\n", + "[13] Frolov, T., et al. (2013). Structural phase transformations in metallic grain boundaries. *Nature Communications*, 4, 1899. https://doi.org/10.1038/ncomms2919\n", "\n", - "[14] Sangiovanni, D. G., Mei, A. B., Edstrom, D., Hultman, L., Chirita, V., Petrov, I., & Greene, J. E. (2018). Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands. Physical Review B, 97(3), 035406. https://doi.org/10.1103/PhysRevB.97.035406\n", + "[14] Sangiovanni, D. G., Mei, A. B., Edström, D., Hultman, L., Chirita, V., Petrov, I., & Greene, J. E. (2018). Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands. Physical Review B, 97(3), 035406. https://doi.org/10.1103/PhysRevB.97.035406\n", "\n", - "[15] Sljivancanin, Z., & Hammer, B. (2002). Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory. *Surface Science*, 515(2-3), 235-244. https://doi.org/10.1016/s0039-6028(02)01908-8\n", + "[15] Šljivančanin, Ž., & Hammer, B. (2002). Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory. *Surface Science*, 515(1), 235-244. https://doi.org/10.1016/s0039-6028(02)01908-8\n", "\n", "[16] Miceli, G., & Pasquarello, A. (2016). Self-compensation due to point defects in Mg-doped GaN. *Physical Review B*, 93(16), 165207. https://doi.org/10.1103/PhysRevB.93.165207\n", "\n", "[17] Togo, A., et al. (2006). First-principles calculations of native defects in tin monoxide. *Physical Review B*, 74(19), 195128. https://doi.org/10.1103/PhysRevB.74.195128\n", "\n", - "[18] Lherbier, A., et al. (2011). Electronic and transport properties of unbalanced sublattice N-doping in graphene. *Physical Review B*, 84(24), 245446. https://doi.org/10.1103/PhysRevB.84.245446\n", + "[18] Fujimoto, Y., & Saito, S. (2011). Formation, stabilities, and electronic properties of nitrogen defects in graphene. *Physical Review B*, 84(24), 245446. https://doi.org/10.1103/PhysRevB.84.245446\n", "\n", - "[19] Ivády, V., et al. (2022). Ab initio theory of the negatively charged boron vacancy qubit in hexagonal boron nitride. *npj Computational Materials*, 8(1), 1-9. https://doi.org/10.1038/s41524-022-00730-w\n", + "[19] Bertoldo, F., Ali, S., Manti, S., & Thygesen, K. S. (2022). Quantum point defects in 2D materials - the QPOD database. *npj Computational Materials*, 8(1), 56. https://doi.org/10.1038/s41524-022-00730-w\n", "\n", "[20] Thompson-Flagg, R. C., et al. (2009). Rippling of graphene. *EPL (Europhysics Letters)*, 85(4), 46002. https://doi.org/10.1209/0295-5075/85/46002\n", "\n", @@ -99,7 +99,10 @@ "[22] Aradi, B., et al. (2007). Theoretical study of the chemical gap tuning in silicon nanowires. *Physical Review B*, 76(3), 035305. https://doi.org/10.1103/PhysRevB.76.035305\n", "\n", "[23] Van de Walle, C. G., & Martin, R. M. (1986). Theoretical calculations of heterojunction discontinuities in the Si/Ge system. *Physical Review B*, 34(8), 5621. https://doi.org/10.1103/PhysRevB.34.5621\n", - "[24] Hinuma, Y., Grüneis, A., Kresse, G., & Oba, F. (2014). Band alignment of semiconductors from density-functional theory and many-body perturbation theory. *Physical Review B*, 90(15), 155405. https://doi.org/10.1103/PhysRevB.90.155405\n" + "\n", + "[24] Hinuma, Y., Grüneis, A., Kresse, G., & Oba, F. (2014). Band alignment of semiconductors from density-functional theory and many-body perturbation theory. *Physical Review B*, 90(15), 155405. https://doi.org/10.1103/PhysRevB.90.155405\n", + "\n", + "[25] Chen, Y., Fang, F., & Zhang, N. (2024). Advance in additive manufacturing of 2D materials at the atomic and close-to-atomic scale. *npj 2D Materials and Applications*, 8(1), 17. https://doi.org/10.1038/s41699-024-00456-x\n" ] }, { diff --git a/other/materials_designer/specific_examples/custom_cutout_etched_silicon.ipynb b/other/materials_designer/specific_examples/custom_cutout_etched_silicon.ipynb index 497ec1f71..5af9d6880 100644 --- a/other/materials_designer/specific_examples/custom_cutout_etched_silicon.ipynb +++ b/other/materials_designer/specific_examples/custom_cutout_etched_silicon.ipynb @@ -13,6 +13,13 @@ "- Two parallel channels at the top\n", "- A deeper central cavity\n", "\n", + "Following the publication:\n", + "\n", + "> **Yixin Chen, Fengzhou Fang, and Nan Zhang**\n", + "> \"Advance in additive manufacturing of 2D materials at the atomic and close-to-atomic scale\"\n", + "> npj 2D Materials and Applications 8, 17 (2024)\n", + "> [DOI: 10.1038/s41699-024-00456-x](https://doi.org/10.1038/s41699-024-00456-x)\n", + "\n", "

Usage

\n", "\n", "1. Make sure to select Input Material (in the outer runtime) before running the notebook.\n", diff --git a/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide.ipynb b/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide.ipynb index 05a9d1d55..c921cfe95 100644 --- a/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide.ipynb +++ b/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide.ipynb @@ -9,7 +9,7 @@ "\n", "This example demonstrates how to create a O interstitial defect in a SnO material. Following the publication:\n", "\n", - "> **A. Togo, F. Oba, and I. Tanaka**\n", + "> **A. Togo, F. Oba, I. Tanaka, and K. Tatsumi**\n", "> \"First-principles calculations of native defects in tin monoxide\"\n", "> Phys. Rev. B 74, 195128 (2006)\n", "> [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128)\n", diff --git a/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide_SIMULATION.ipynb b/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide_SIMULATION.ipynb index 9f8e84d39..5b5a7cf1f 100644 --- a/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide_SIMULATION.ipynb +++ b/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide_SIMULATION.ipynb @@ -7,7 +7,7 @@ "source": [ "# Formation Energy and DOS of the V_Sn-O_i Defect Pair in SnO\n", "\n", - "> **A. Togo, F. Oba, and I. Tanaka**\n", + "> **A. Togo, F. Oba, I. Tanaka, and K. Tatsumi**\n", "> \"First-principles calculations of native defects in tin monoxide\"\n", "> Phys. Rev. B 74, 195128 (2006)\n", "> [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128)\n", @@ -718,7 +718,7 @@ "source": [ "## References\n", "\n", - "[1] Togo, A., Oba, F., & Tanaka, I. (2006). First-principles calculations of native defects in tin monoxide. Phys. Rev. B, 74(19), 195128. https://doi.org/10.1103/PhysRevB.74.195128" + "[1] Togo, A., Oba, F., Tanaka, I., & Tatsumi, K. (2006). First-principles calculations of native defects in tin monoxide. Phys. Rev. B, 74(19), 195128. https://doi.org/10.1103/PhysRevB.74.195128" ] } ], diff --git a/other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb b/other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb index f78e5f2b6..607861b0f 100644 --- a/other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb +++ b/other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb @@ -13,7 +13,7 @@ "\n", "[//]: # ()\n", "\n", - "> **Yoshitaka Fujimoto and Susumu Saito**, \"Formation, stabilities, and electronic properties of nitrogen defects in graphene\", Physical Review B, 2011. [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446).\n", + "> **Yoshitaka Fujimoto and Susumu Saito**, \"Formation, stabilities, and electronic properties of nitrogen defects in graphene\", Physical Review B 84, 245446 (2011). [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446).\n", "> \n", "Below is the figure 1 from the manuscript demonstrating the nitrogen substitution defects in graphene.\n", "\n", diff --git a/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride.ipynb b/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride.ipynb index b1f58e76a..a992d8ff0 100644 --- a/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride.ipynb +++ b/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride.ipynb @@ -12,7 +12,7 @@ "This tutorial demonstrates the process of creating materials with vacancy defects, based on the work presented in the following manuscript:\n", "\n", "> **Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen**,\n", - "> \"Quantum point defects in 2D materials - the QPOD database\", npj Computational Materials, 2022. \n", + "> \"Quantum point defects in 2D materials - the QPOD database\", npj Computational Materials 8, 56 (2022). \n", "> [DOI:10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w)\n", "\n", "Below is the figure 1 from the manuscript demonstrating the boron vacancy defects in hexagonal boron nitride (h-BN).\n", diff --git a/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynb b/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynb index 72cc22ced..daed21210 100644 --- a/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynb +++ b/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynb @@ -8,7 +8,7 @@ "# Defect Formation Energy of a Boron Vacancy in h-BN\n", "\n", "> **Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen**,\n", - "> \"Quantum point defects in 2D materials - the QPOD database\", npj Computational Materials, 2022.\n", + "> \"Quantum point defects in 2D materials - the QPOD database\", npj Computational Materials 8, 56 (2022).\n", "> [DOI:10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w)\n", "\n", "Computes the neutral formation energy of the vacancy created in the\n", @@ -723,7 +723,7 @@ "source": [ "## References\n", "\n", - "[1] Bertoldo, Ali, Manti & Thygesen, \"Quantum point defects in 2D materials — the QPOD database\", npj Comput. Mater. 8, 56 (2022). https://doi.org/10.1038/s41524-022-00730-w\n", + "[1] Bertoldo, Ali, Manti & Thygesen, \"Quantum point defects in 2D materials - the QPOD database\", npj Comput. Mater. 8, 56 (2022). https://doi.org/10.1038/s41524-022-00730-w\n", "[2] QPOD entry v_B in BN (charge 0): https://qpod.fysik.dtu.dk/material/1BN-1.2d.v_B.0.1" ] } diff --git a/other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb b/other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb index c065a3e46..fb0a12959 100644 --- a/other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb +++ b/other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb @@ -12,7 +12,7 @@ "This tutorial demonstrates creation of metal adatom on graphene hollow site.\n", "\n", "> **Chan, K. T., Neaton, J. B., & Cohen, M. L. (2008).** \n", - "> First-principles study of metal adatom adsorption on graphene. Physical Review B, 77(23). \n", + "> First-principles study of metal adatom adsorption on graphene. Physical Review B, 77(23), 235430. \n", "> [DOI:10.1103/physrevb.77.235430 ](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.77.235430)\n", " \n", "\n", diff --git a/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb b/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb index 0cb6cf936..7e9216ac5 100644 --- a/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb +++ b/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb @@ -12,7 +12,7 @@ "This tutorial demonstrates the process of creating a rectangular island defect on a slab. \n", "\n", "\n", - "> **D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene**, \"Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands\", Physical Review B, 2018. [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406).\n", + "> **D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene**, \"Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands\", Physical Review B 97, 035406 (2018). [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406).\n", "> \n", "\n", "![Fig 2.](https://github.com/Exabyte-io/documentation/raw/12617167278ae3523adc028583b21ea4e8ebd197/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png)\n", diff --git a/other/materials_designer/specific_examples/defect_surface_step_platinum.ipynb b/other/materials_designer/specific_examples/defect_surface_step_platinum.ipynb index 8cc9d0028..12dd616fa 100644 --- a/other/materials_designer/specific_examples/defect_surface_step_platinum.ipynb +++ b/other/materials_designer/specific_examples/defect_surface_step_platinum.ipynb @@ -13,8 +13,8 @@ "\n", "> **Šljivančanin, Ž., & Hammer, B.**\n", "> \"Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory.\"\n", - "> Surface Science, 515(1), 235–244. \n", - "> [DOI: 10.1016/s0039-6028(02)01908-8 ](https://doi:10.1016/s0039-6028(02)01908-8 )\n", + "> Surface Science, 515(1), 235–244 (2002). \n", + "> [DOI: 10.1016/s0039-6028(02)01908-8](https://doi.org/10.1016/s0039-6028(02)01908-8)\n", "\n", "Replicating the material from the FIG. 1. B.\n", "\n", diff --git a/other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb b/other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb index b27cccfb7..d7ebc0bfe 100644 --- a/other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb +++ b/other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb @@ -12,8 +12,8 @@ "\n", "Following the manuscript:\n", " > **Shan, T.-R., Devine, B. D., Phillpot, S. R., & Sinnott, S. B.** \n", - " > \"Molecular dynamics study of the adhesion of Cu/SiO2interfaces using a variable-charge interatomic potential.\"\n", - " > Physical Review B, 83(11). \n", + " > \"Molecular dynamics study of the adhesion of Cu/SiO2 interfaces using a variable-charge interatomic potential.\"\n", + " > Physical Review B, 83(11), 115327 (2011). \n", " > [DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327) \n", "\n", "\n", diff --git a/other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb b/other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb index 3fb5e1926..932b2d730 100644 --- a/other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb +++ b/other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb @@ -1072,7 +1072,7 @@ "source": [ "## References\n", "\n", - "[1] Arjun Dahal, Matthias Batzill, \"Graphene-nickel interfaces: a review\",\n", + "[1] Arjun Dahal, Matthias Batzill, \"Graphene–nickel interfaces: a review\",\n", "Nanoscale 6(5), 2548 (2014). [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f)\n", "\n", "[2] Jayeeta Lahiri, Travis S. Miller, Andrew J. Ross, Lyudmyla Adamska, Ivan I. Oleynik,\n",