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Materials Project Validation, Provenance, and Sandboxes by Dan Gunter

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Dan Gunter
Dan Gunter

Summary of Goals, Progress, and Next steps for these three aspects of the Materials Project (materialsproject.org) infrastructure * Validation: constantly guard against bugs in core data and imported data * Provenance: know how data came to be * Sandboxes: combine public and non-public data; "good fences make good neighbors" Presenter: Dan Gunter, LBNL

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The Materials Project Validation, Provenance and Sandboxes
Goals ‱ Validation – constantly guard against bugs in core data and imported data ‱ Provenance – know how data came to be ‱ Sandboxes – Combine public and non-public data; "good fences make good neighbors"
Validation (Internal) Database ID External ID What we expected What we got
Validation runs all the time ‱ Rules with "constraints" for every database (and sandbox) ‱ Test constraints against entire DB every night  email reports ‱ Validation engine, etc. all open-source software in pymatgen-db Remote server Validation engine Rules MP Databases Reports (email, web pages, ..)
Rules have a simple syntax _aliases: - snl_id = mps_id - energy = analysis.e_above_hull materials: - filter: constraints: - final_energy_per_atom <= 0 - initial_structure.lattice.volume > 0 - initial_structure.lattice.a > 0 - initial_structure.lattice.b > 0 - initial_structure.lattice.c > 0 - initial_structure.lattice.matrix size 3 - formation_energy_per_atom <= 5 - formation_energy_per_atom > -5 - cpu_time > 5 - e_above_hull > -0.000001 - final_energy < 0 - reduced_cell_formula size$ nelements # Check num. ICSD sources for selected compounds - filter: - task_id = "mp-540081" constraints: - icsd_id size> 10 - filter: - task_id = "mp-20379" constraints: - icsd_id size 1 - filter: - task_id = "mp-13634" constraints: - icsd_id size> 0 - filter: - task_id = "mp-600022" constraints: - icsd_id size 0 # NiO2 phases should never become stable - filter: - e_above_hull = 0 constraints: - pretty_formula != 'NiO2' tasks: - filter: - state = "successful" constraints: - output.final_energy_per_atom <= 0
Validation summary Easy-to-use, integrated, efficient tools to report errors Next steps – Record all check results in DB – More sophisticated checks (Map/Reduce) – Make it easier to add new checks internally – Make it easier to add new check for anyone ‱ per-sandbox or even per-user ("MP Alerts")
Provenance: How do I know that the data is correct?
Types of provenance in the system 1) Calculation workflows – FireWorks records calculation inputs, .. results in great detail 2) External datasets – Structure Notation Language standardizes the naming of data sources and publications 3) Post-calculation data transformations – New "builders" provides framework for tracking creation of final database products (1) (2) (3)
Provenance is available for every material
Provenance in DB Structure Notation Language "snl_final": { "about": { "created_at": { "string": "2014-02-22 19:07:00.383869", "@class": "datetime", "@module": "datetime" }, "_materialsproject": { "submission_id": 52621, "snl_id": 398676, "spacegroup": { "lattice_type": "tetragonal", "symbol": "P4_2/mmc", "number": 131, "point_group": "4/mmm", "crystal_system": "tetragonal", "hall": "-P 4c 2" } }, "_cedergroup": { "BURP_sids": [ 409544, 409545, 409546 ], "icsd_ids": [ ], "e_above_hull": 0.075125350000000423734 }, "references": "", "authors": [ { "name": "Geoffroy Hautier", "email": "geoffroy.hautier@uclouvain .be" }, { "name": "Bo Xu", "email": "boxu14@mit.edu" } ], "remarks": [ "supplementary compounds from MIT matgen database" ], "projects": [ "MIT matgen" ], "history": [ { "url": "http://www.fiz- karlsruhe.de/icsd_home.htm l", "name": "Inorganic Crystal Structure Database", "description": { "Collection code": 24692 } }, { "url": "", "name": "", "description": { "source": null, "orig_name": "Basic substitution code.", "formula": "O1 Pd1" } }, { "url": "http://ceder.mit.edu/", "name": "MIT Ceder group research database", "description": { "source": 105986, "orig_name": "", "formula": "FeO" } }, { "url": "http://www.materialsproject. org", "name": "Materials Project structure optimization", "description": { "fw_id": 820305, "task_type": "GGA optimize structure (2x)", "task_id": "mp- 753682" } }, { "url": "http://www.materialsproject. org", "name": "Materials Project structure optimization", "description": { "fw_id": 820308, "task_type": "GGA+U optimize structure (2x)", "task_id": "mp- 776678" } } ] }, Metadata Crystal DB sources References History of structure optimizations
Future work: unified view of provenance VASP result ICSD VASP result VASP result Post- processing Material properties Computation Data import processing e.g., Defects
Sandbox example: Multivalent JCESR users Non- JCESR users
Multivalent app
Sandboxes = Database + Apps Core data Core data + multivalent materials Non- JCESR users JCESR users
Technical challenges ‱ Pre-process data for real-time search ‱ Interfaces for per-user access control – https://materialsproject.org/materials/1234?san dbox=jcesr – Web UI elements and
Future: dynamic sandbox creation Current: – Large & significant additional data / apps ‱ e.g., JCESR – Longer-term connections to MP data ‱ e.g. porous materials – Companies ‱ e.g. VW/Stanford Future small collab. per-user? CoD?
Summary ‱ Validation – guard against bugs by checking all data daily and at data import/creation time ‱ Provenance – universal standard for annotating data provenance ‱ Sandboxes – unified view of distinct databases – onramp for new collaborations and data

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Materials Project Validation, Provenance, and Sandboxes by Dan Gunter

  • 1. The Materials Project Validation, Provenance and Sandboxes
  • 2. Goals ‱ Validation – constantly guard against bugs in core data and imported data ‱ Provenance – know how data came to be ‱ Sandboxes – Combine public and non-public data; "good fences make good neighbors"
  • 3. Validation (Internal) Database ID External ID What we expected What we got
  • 4. Validation runs all the time ‱ Rules with "constraints" for every database (and sandbox) ‱ Test constraints against entire DB every night  email reports ‱ Validation engine, etc. all open-source software in pymatgen-db Remote server Validation engine Rules MP Databases Reports (email, web pages, ..)
  • 5. Rules have a simple syntax _aliases: - snl_id = mps_id - energy = analysis.e_above_hull materials: - filter: constraints: - final_energy_per_atom <= 0 - initial_structure.lattice.volume > 0 - initial_structure.lattice.a > 0 - initial_structure.lattice.b > 0 - initial_structure.lattice.c > 0 - initial_structure.lattice.matrix size 3 - formation_energy_per_atom <= 5 - formation_energy_per_atom > -5 - cpu_time > 5 - e_above_hull > -0.000001 - final_energy < 0 - reduced_cell_formula size$ nelements # Check num. ICSD sources for selected compounds - filter: - task_id = "mp-540081" constraints: - icsd_id size> 10 - filter: - task_id = "mp-20379" constraints: - icsd_id size 1 - filter: - task_id = "mp-13634" constraints: - icsd_id size> 0 - filter: - task_id = "mp-600022" constraints: - icsd_id size 0 # NiO2 phases should never become stable - filter: - e_above_hull = 0 constraints: - pretty_formula != 'NiO2' tasks: - filter: - state = "successful" constraints: - output.final_energy_per_atom <= 0
  • 6. Validation summary Easy-to-use, integrated, efficient tools to report errors Next steps – Record all check results in DB – More sophisticated checks (Map/Reduce) – Make it easier to add new checks internally – Make it easier to add new check for anyone ‱ per-sandbox or even per-user ("MP Alerts")
  • 7. Provenance: How do I know that the data is correct?
  • 8. Types of provenance in the system 1) Calculation workflows – FireWorks records calculation inputs, .. results in great detail 2) External datasets – Structure Notation Language standardizes the naming of data sources and publications 3) Post-calculation data transformations – New "builders" provides framework for tracking creation of final database products (1) (2) (3)
  • 10. Provenance in DB Structure Notation Language "snl_final": { "about": { "created_at": { "string": "2014-02-22 19:07:00.383869", "@class": "datetime", "@module": "datetime" }, "_materialsproject": { "submission_id": 52621, "snl_id": 398676, "spacegroup": { "lattice_type": "tetragonal", "symbol": "P4_2/mmc", "number": 131, "point_group": "4/mmm", "crystal_system": "tetragonal", "hall": "-P 4c 2" } }, "_cedergroup": { "BURP_sids": [ 409544, 409545, 409546 ], "icsd_ids": [ ], "e_above_hull": 0.075125350000000423734 }, "references": "", "authors": [ { "name": "Geoffroy Hautier", "email": "geoffroy.hautier@uclouvain .be" }, { "name": "Bo Xu", "email": "boxu14@mit.edu" } ], "remarks": [ "supplementary compounds from MIT matgen database" ], "projects": [ "MIT matgen" ], "history": [ { "url": "http://www.fiz- karlsruhe.de/icsd_home.htm l", "name": "Inorganic Crystal Structure Database", "description": { "Collection code": 24692 } }, { "url": "", "name": "", "description": { "source": null, "orig_name": "Basic substitution code.", "formula": "O1 Pd1" } }, { "url": "http://ceder.mit.edu/", "name": "MIT Ceder group research database", "description": { "source": 105986, "orig_name": "", "formula": "FeO" } }, { "url": "http://www.materialsproject. org", "name": "Materials Project structure optimization", "description": { "fw_id": 820305, "task_type": "GGA optimize structure (2x)", "task_id": "mp- 753682" } }, { "url": "http://www.materialsproject. org", "name": "Materials Project structure optimization", "description": { "fw_id": 820308, "task_type": "GGA+U optimize structure (2x)", "task_id": "mp- 776678" } } ] }, Metadata Crystal DB sources References History of structure optimizations
  • 11. Future work: unified view of provenance VASP result ICSD VASP result VASP result Post- processing Material properties Computation Data import processing e.g., Defects
  • 14. Sandboxes = Database + Apps Core data Core data + multivalent materials Non- JCESR users JCESR users
  • 15. Technical challenges ‱ Pre-process data for real-time search ‱ Interfaces for per-user access control – https://materialsproject.org/materials/1234?san dbox=jcesr – Web UI elements and
  • 16. Future: dynamic sandbox creation Current: – Large & significant additional data / apps ‱ e.g., JCESR – Longer-term connections to MP data ‱ e.g. porous materials – Companies ‱ e.g. VW/Stanford Future small collab. per-user? CoD?
  • 17. Summary ‱ Validation – guard against bugs by checking all data daily and at data import/creation time ‱ Provenance – universal standard for annotating data provenance ‱ Sandboxes – unified view of distinct databases – onramp for new collaborations and data

Hinweis der Redaktion

  1. Picture of 1915 Heinrich Campendonk painting, "Landscape with horses". Steve Martin paid $850K for a forged version of the painting, from a reputable art house in Paris, in 2004. He sold it at a loss of $250K before discovering it was a forgery. The forgery was performed by Wolfgang Beltracchi.
  2. Sandboxes are a way to share preliminary data in the context of MP data and tools.