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VsevolodX merged 10 commits into from
Mar 20, 2026
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update: restructure according to MCODE #280

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0db506f
update: restructure according to MCODE
VsevolodX Mar 19, 2026
d977922
update: cleanup
VsevolodX Mar 19, 2026
9332d4b
update: mcode for generic NBs
VsevolodX Mar 20, 2026
d51b4a2
update: correct categories
VsevolodX Mar 20, 2026
4f22982
chore: address pr comment
VsevolodX Mar 20, 2026
3fcde1f
chore: add mcode spelling out
VsevolodX Mar 20, 2026
b243fac
chore: correction
VsevolodX Mar 20, 2026
f76727a
update: adjust table
VsevolodX Mar 20, 2026
94e016d
update: add references
VsevolodX Mar 20, 2026
535208f
update: add doi
VsevolodX Mar 20, 2026
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99 changes: 46 additions & 53 deletions other/materials_designer/Introduction.ipynb
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Expand Up @@ -10,80 +10,77 @@
"source": [
"# Contents.\n",
"\n",
"This document contains links to the functionality listed.\n",
"This document contains links to the functionality listed. Section numbers follow **Domain (`X`) → Dimensionality (`X.Y`) → Category (`X.Y.Z`)**, with **M-CODE** labels aligned to the MCODE taxonomy ([arxiv](https://arxiv.org/abs/2602.14384)).\n",
"\n",
"## 1. Single-Material Structures.\n",
"\n",
"### 1.1. 3D Structures.\n",
"#### [1.1.1. Supercells. Create supercells from 3D crystals.](create_supercell.ipynb)\n",
"## 1. Pristine Structures.\n",
"\n",
"### 1.2. 2D Structures.\n",
"#### [1.2.1. Slabs. Create a slab from a bulk material.](create_slab.ipynb)\n",
"#### [1.2.2. Monolayers. Create a monolayer from a bulk material.](create_monolayer.ipynb)\n",
"### 1.1. 3D\n",
"#### [1.1.1. Supercells. Create supercells from 3D crystals. `P-3D-CRY`](create_supercell.ipynb)\n",
"\n",
"### 1.3. 1D Structures.\n",
"#### [1.3.1. Nanoribbons. Create nanoribbons from 2D materials.](create_nanoribbon.ipynb)\n",
"#### [1.3.2. Nanowires. Create a nanowire from a bulk material.](create_nanowire.ipynb)\n",
"#### [1.3.3. Nanowires with custom shape. Create a nanowire with a custom cross-section.](create_nanowire_custom_shape.ipynb)\n",
"### 1.2. 2D\n",
"#### [1.2.1. Slabs. Create a slab from a bulk material. `P-2D-SLB`](create_slab.ipynb)\n",
"#### [1.2.2. Monolayers. Create a monolayer from a bulk material. `P-2D-MNL`](create_monolayer.ipynb)\n",
"\n",
"### 1.4. 0D Structures.\n",
"#### [1.4.1. Spherical Cluster. Create a spherical cluster from a bulk material.](create_cluster_sphere.ipynb)\n",
"#### [1.4.2. Custom Shape Cluster. Create a cluster by cutting it out of a slab.](create_cluster_custom_shape.ipynb)\n",
"#### [1.4.3. Specific Shape Cluster. Create a cluster by building up a specific shape.](create_cluster_specific_shape.ipynb)\n",
"#### [1.4.4. Box-cutout. Create a slab with a box cutout](create_cutout_box.ipynb)\n",
"#### [1.4.5. Custom Shape Cutout. Create a slab with a custom shape cutout.](create_cutout_custom_shape.ipynb)\n",
"### 1.3. 1D\n",
"#### [1.3.1. Nanowires. Create a nanowire from a bulk material. `P-1D-NWR`](create_nanowire.ipynb)\n",
"#### [1.3.2. Nanowires with custom shape. Create a nanowire with a custom cross-section. `P-1D-NWR`](create_nanowire_custom_shape.ipynb)\n",
"\n",
"### 1.4. 0D\n",
"#### [1.4.1. Nanoribbons. Create nanoribbons from 2D materials. `P-0D-NRB`](create_nanoribbon.ipynb)\n",
"#### [1.4.2. Spherical Cluster. Create a spherical cluster from a bulk material. `P-0D-NPR`](create_cluster_sphere.ipynb)\n",
"#### [1.4.3. Custom Shape Cluster. Create a cluster by cutting it out of a slab. `P-0D-NPR`](create_cluster_custom_shape.ipynb)\n",
"#### [1.4.4. Specific Shape Cluster. Create a cluster by building up a specific shape. `P-0D-NPR`](create_cluster_specific_shape.ipynb)\n",
"#### [1.4.5. Box-cutout. Create a slab with a box cutout `X-0D-CUT`](create_cutout_box.ipynb)\n",
"#### [1.4.6. Custom Shape Cutout. Create a slab with a custom shape cutout. `X-0D-CUT`](create_cutout_custom_shape.ipynb)\n",
"\n",
"## 2. Multi-Material Structures.\n",
"\n",
"### 2.1. Interfaces\n",
"#### [2.1.1. Interface with Zur and McGill Superlattice (ZSL) strain matching](create_interface_with_min_strain_zsl.ipynb)\n",
"## 2. Compound Pristine Structures.\n",
"\n",
"#### [2.1.3. Interface without strain matching](create_interface_with_no_strain_matching.ipynb)\n",
"### 2.1. 2D\n",
"#### [2.1.1. Interface with Zur and McGill Superlattice (ZSL) strain matching `C-2D-INT-Z`](create_interface_with_min_strain_zsl.ipynb)\n",
"#### [2.1.3. Interface without strain matching `C-2D-INT-Z`](create_interface_with_no_strain_matching.ipynb)\n",
"#### [2.1.2. Interface with ASE EMT Relaxation `C-2D-INT-Z`](create_interface_with_relaxation_ase_emt.ipynb)\n",
"#### [2.1.4. Twisted Interface with Commensurate Lattices `C-2D-INT-C`](create_twisted_interface_with_commensurate_lattices.ipynb)\n",
"#### [2.1.5. Heterostructure with multiple consecutive layers `C-2D-HST`](create_heterostructure_example.ipynb)\n",
"#### [2.1.6. Optimize film position on interface `C-2D-INT-Z`](optimize_film_position.ipynb).\n",
"\n",
"#### [2.1.2. Interface with ASE EMT Relaxation](create_interface_with_relaxation_ase_emt.ipynb)\n",
"### 2.2. 0D\n",
"#### [2.2.1. Twisted Nanoribbon Interface/Stack `C-0D-INT-R`](create_twisted_interface_with_nanoribbons.ipynb)\n",
"\n",
"#### [2.1.4. Twisted Interface with Commensurate Lattices](create_twisted_interface_with_commensurate_lattices.ipynb)\n",
"\n",
"### 2.2. Stacked Nanoribbons\n",
"#### [2.2.1. Twisted Nanoribbon Interface/Stack](create_twisted_interface_with_nanoribbons.ipynb)\n",
"## 3. Defective Structures.\n",
"\n",
"### 2.3. Heterostructures\n",
"#### [2.3.1. Heterostructure with multiple consecutive layers](create_heterostructure_example.ipynb)\n",
"### 3.1. 2D\n",
"#### [3.1.1. Adatom Defect on a Slab `D-2D-ADA`](create_adatom_defect.ipynb)\n",
"#### [3.1.2. Terrace Defect on a Slab `D-2D-TER`](create_terrace_defect.ipynb)\n",
"#### [3.1.3. Grain Boundary Planar `D-2D-GBL`](create_grain_boundary_crystal.ipynb)\n",
"\n",
"### 3.2. 1D\n",
"#### [3.2.1. Grain Boundary Linear `D-1D-GBP`](create_grain_boundary_film.ipynb)\n",
"\n",
"## 3. Defects.\n",
"\n",
"### 3.1. Point Defects\n",
"#### [3.1.1. Point Defects: vacancy, substitution, interstitial](create_point_defect.ipynb)\n",
"#### [3.1.2. Point Defects Pair](create_point_defect_pair.ipynb)\n",
"\n",
"### 3.2. Surface Defects\n",
"#### [3.2.1. Adatom Defect on a Slab](create_adatom_defect.ipynb)\n",
"#### [3.2.2. Terrace Defect on a Slab](create_terrace_defect.ipynb)\n",
"\n",
"### 3.3. Planar Defects\n",
"#### [3.3.1. Grain Boundary in a 3D Crystal](create_grain_boundary_crystal.ipynb)\n",
"#### [3.3.2. Grain Boundary in a 2D Material](create_grain_boundary_film.ipynb)\n",
"### 3.3. 0D\n",
"#### [3.3.1. Point Defects: vacancy, substitution, interstitial `D-0D-SUB` · `D-0D-VAC` · `D-0D-INT`](create_point_defect.ipynb)\n",
"#### [3.3.2. Point Defects Pair `D-0D-DFP`](create_point_defect_pair.ipynb)\n",
"\n",
"\n",
"## 4. Passivation.\n",
"\n",
"### 4.1. Surface Passivation\n",
"#### [4.1.1. Slab Passivation](passivate_slab.ipynb) \n",
"### 4.1. 2D\n",
"#### [4.1.1. Slab Passivation `X-2D-PAS`](passivate_slab.ipynb) \n",
"\n",
"### 4.2. Edge Passivation\n",
"#### [4.2.1. Edge Passivation](passivate_edge.ipynb)\n",
"### 4.2. 1D\n",
"#### [4.2.1. Edge Passivation `X-1D-PAS`](passivate_edge.ipynb)\n",
"\n",
"\n",
"## 5. Perturbations.\n",
"\n",
"### 5.1. Slab Perturbations\n",
"#### [5.1.1. Perturbation using sine wave](create_perturbation.ipynb)\n",
"#### [5.1.2. Perturbation using custom function](create_perturbation_custom.ipynb)\n",
"### 5.1. 3D\n",
"#### [5.1.1. Maxwell-Boltzmann thermal disorder `X-3D-PER`](create_maxwell_disorder.ipynb)\n",
"\n",
"### 5.2. Thermal Disorder\n",
"#### [5.2.1. Maxwell-Boltzmann thermal disorder](create_maxwell_disorder.ipynb)\n",
"### 5.2. 2D\n",
"#### [5.2.1. Perturbation using sine wave `X-2D-PER`](create_perturbation.ipynb)\n",
"#### [5.2.2. Perturbation using custom function `X-2D-PER`](create_perturbation_custom.ipynb)\n",
"\n",
"\n",
"## 6. Other.\n",
Expand All @@ -100,10 +97,6 @@
"\n",
"This notebook demonstrates a workflow for converting materials data from the [JARVIS](https://jarvis.nist.gov/) database into ESSE format for use with the Mat3ra.com platform.\n",
"\n",
"## 6.2. Optimize.\n",
"\n",
"#### [6.2.1. Optimize film position on interface](optimize_film_position.ipynb).\n",
"\n",
"## 6.3. Development.\n",
"\n",
"#### [6.3.1. Custom Transformation](custom_transformation.ipynb). Notebook setup for development of custom transformations on materials.\n",
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