Materials Genomics
Unit 3: Materials Databases and Thermodynamic Quantities

Prof. Dr. Philipp Pelz

FAU Erlangen-Nürnberg

01. Title: Materials Databases and Thermodynamic Quantities

• Frame the unit in the end-to-end materials discovery workflow and state the decision problems it addresses.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

02. Learning objectives and expected outputs

• State measurable outcomes (what students can explain, implement, and critique by the end of the unit).
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

03. Recap from previous unit and dependency map

• Reconnect prerequisite concepts from earlier units and make dependency assumptions explicit.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

04. Why this unit matters for materials discovery

• Motivate with a realistic failure/success scenario from materials discovery practice.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

05. Reading map and chapter anchors

• Map slide blocks to the key book chapters so students can pre-read and post-review effectively.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

06. Materials Project, OQMD, AFLOW, NOMAD: scope and differences

• Explain materials project, oqmd, aflow, nomad: scope and differences using one concrete materials example and one common failure mode.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

07. What a materials record contains: composition, structure, method metadata

• Compare what a materials record contains: composition, structure, method metadata using one concrete materials example and one common failure mode.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

08. CIF vs POSCAR vs JSON schema fields

• Diagnose cif vs poscar vs json schema fields using one concrete materials example and one common failure mode.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

09. Thermodynamic targets: formation energy, energy above hull, free energy

• Apply thermodynamic targets: formation energy, energy above hull, free energy using one concrete materials example and one common failure mode.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

10. Convex hull construction and physical interpretation

• Define convex hull construction and physical interpretation using one concrete materials example and one common failure mode.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

11. Metastability windows and practical screening thresholds

• Explain metastability windows and practical screening thresholds using one concrete materials example and one common failure mode.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

12. Phase stability vs synthesizability distinction

• Compare phase stability vs synthesizability distinction using one concrete materials example and one common failure mode.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

13. Computational settings (functional, cutoff, k-mesh) as hidden confounders

• Diagnose computational settings (functional, cutoff, k-mesh) as hidden confounders using one concrete materials example and one common failure mode.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

14. Reference states and consistent energy normalization

• Apply reference states and consistent energy normalization using one concrete materials example and one common failure mode.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

15. Query APIs and reproducible data snapshots

• Define query apis and reproducible data snapshots using one concrete materials example and one common failure mode.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

16. Database joins: structure table + property table + provenance

• Explain database joins: structure table + property table + provenance using one concrete materials example and one common failure mode.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

17. Handling duplicates, polymorphs, and near-duplicate structures

• Compare handling duplicates, polymorphs, and near-duplicate structures using one concrete materials example and one common failure mode.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

18. Missing-value patterns in computed materials datasets

• Diagnose missing-value patterns in computed materials datasets using one concrete materials example and one common failure mode.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

19. Unit harmonization and dimensional consistency checks

• Apply unit harmonization and dimensional consistency checks using one concrete materials example and one common failure mode.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

20. Data leakage via family overlap in random splits

• Define data leakage via family overlap in random splits using one concrete materials example and one common failure mode.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

21. Grouped splits by composition family or prototype

• Explain grouped splits by composition family or prototype using one concrete materials example and one common failure mode.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

22. Outlier detection: physics outlier vs parsing/ETL error

• Compare outlier detection: physics outlier vs parsing/etl error using one concrete materials example and one common failure mode.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

23. Train/validation/test design for discovery tasks

• Diagnose train/validation/test design for discovery tasks using one concrete materials example and one common failure mode.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

24. Target definition quality for bandgap and stability tasks

• Apply target definition quality for bandgap and stability tasks using one concrete materials example and one common failure mode.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

25. Correlation traps in periodic-table-driven descriptors

• Define correlation traps in periodic-table-driven descriptors using one concrete materials example and one common failure mode.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

26. Bias from successful-publication and stable-compound overrepresentation

• Explain bias from successful-publication and stable-compound overrepresentation using one concrete materials example and one common failure mode.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

27. How database incompleteness affects model confidence

• Compare how database incompleteness affects model confidence using one concrete materials example and one common failure mode.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

28. Minimal data card for a materials ML dataset

• Diagnose minimal data card for a materials ml dataset using one concrete materials example and one common failure mode.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

29. Provenance logging for reproducibility and trust

• Apply provenance logging for reproducibility and trust using one concrete materials example and one common failure mode.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

30. Practical ETL pipeline from raw files to model table

• Define practical etl pipeline from raw files to model table using one concrete materials example and one common failure mode.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

31. Versioning database dumps and notebook environments

• Explain versioning database dumps and notebook environments using one concrete materials example and one common failure mode.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

32. Sanity baselines before training any complex model

• Compare sanity baselines before training any complex model using one concrete materials example and one common failure mode.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

33. Interpreting uncertainty when labels are computed quantities

• Diagnose interpreting uncertainty when labels are computed quantities using one concrete materials example and one common failure mode.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

34. Quality gates before moving to representation learning

• Apply quality gates before moving to representation learning using one concrete materials example and one common failure mode.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

35. How this unit supports Unit 4 descriptor engineering

• Define how this unit supports unit 4 descriptor engineering using one concrete materials example and one common failure mode.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

36. Common failure mode: hull labels without consistent references

• Explain common failure mode: hull labels without consistent references using one concrete materials example and one common failure mode.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

37. Common failure mode: hidden split leakage through polymorph IDs

• Compare common failure mode: hidden split leakage through polymorph ids using one concrete materials example and one common failure mode.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

38. Advanced note: Materials Databases and Thermodynamic Quantities concept extension 33

• Diagnose advanced note: materials databases and thermodynamic quantities concept extension 33 using one concrete materials example and one common failure mode.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

39. Advanced note: Materials Databases and Thermodynamic Quantities concept extension 34

• Apply advanced note: materials databases and thermodynamic quantities concept extension 34 using one concrete materials example and one common failure mode.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

40. Advanced note: Materials Databases and Thermodynamic Quantities concept extension 35

• Define advanced note: materials databases and thermodynamic quantities concept extension 35 using one concrete materials example and one common failure mode.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

41. Advanced note: Materials Databases and Thermodynamic Quantities concept extension 36

• Explain advanced note: materials databases and thermodynamic quantities concept extension 36 using one concrete materials example and one common failure mode.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

42. Advanced note: Materials Databases and Thermodynamic Quantities concept extension 37

• Compare advanced note: materials databases and thermodynamic quantities concept extension 37 using one concrete materials example and one common failure mode.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

43. Advanced note: Materials Databases and Thermodynamic Quantities concept extension 38

• Diagnose advanced note: materials databases and thermodynamic quantities concept extension 38 using one concrete materials example and one common failure mode.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

44. Advanced note: Materials Databases and Thermodynamic Quantities concept extension 39

• Apply advanced note: materials databases and thermodynamic quantities concept extension 39 using one concrete materials example and one common failure mode.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

45. Exercise setup and dataset definition

• Define dataset, split protocol, and expected deliverables before any coding begins.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].

46. Exercise task 1 (pipeline core)

• Implement the core pipeline component with reproducible settings and documented assumptions.
• Applied anchor: querying MP for bandgap+E_hull.
• Book anchor: [Sandfeld 2.2].

47. Exercise task 2 (comparison/ablation)

• Run an ablation/comparison under identical validation protocol and interpret differences.
• Applied anchor: joining CIF with computed targets.
• Book anchor: [Neuer 4.2.2].

48. Exercise task 3 (failure analysis)

• Perform structured failure analysis and propose one evidence-backed mitigation.
• Applied anchor: filtering by stability threshold.
• Book anchor: [Neuer 4.4.1].

49. Exam-oriented key statements

• Summarize high-yield statements in concise written-exam style with definitions and caveats.
• Applied anchor: grouped split by prototype.
• Book anchor: [McClarren Ch4].

50. Summary, next-unit bridge, and references

• Consolidate the unit into a checklist: concepts, pitfalls, and decisions for next-unit transfer.
• Applied anchor: detecting duplicate polymorph entries.
• Book anchor: [Bishop 3.1–3.3].