Added the latest version 2.3 and 2.4 of ReSpecTh data by LekiaAnonim · Pull Request #35 · pr-omethe-us/ChemKED-database

LekiaAnonim · 2026-03-28T01:33:46Z

Changes proposed in this pull request:

Added 3,596 ChemKED YAML files converted from ReSpecTh v2.3/v2.4 indirect experiment data across 12 fuel categories: ammonia, butanol, ethanol, ethylene, hydrogen, methane, methanol, methanol_NOx, pentane, syngas, syngas_NOx, and H2_O2_NOx
Files span 6 experiment types: ignition delay (1,423), laminar burning velocity measurement (1,462), concentration time profile measurement (287), outlet concentration measurement (178), jet stirred reactor measurement (158), and burner stabilized flame speciation measurement (88)
Data sourced from 1,060 unique references, organised in fuel/Author_Year/ directory structure
All composition data normalised to mole fraction; LaTeX-encoded author names decoded to Unicode
Conversion performed using pyked.batch_convert (see companion PR in PyKED)

Copilot

Pull request overview

Adds newly converted ChemKED YAML datasets from ReSpecTh v2.3/v2.4, expanding the repository’s indirect experiment coverage across multiple fuels and experiment types.

Changes:

Introduces new ChemKED YAML experiment files for H2/O2/NOx-related datasets (shock tube, flow reactor, jet-stirred reactor, and burner-stabilized flame data).
Encodes common-properties (e.g., composition, pressure, ignition-type) and per-datapoint measured quantities in a consistent ChemKED structure.
Standardizes composition basis to mole fraction and embeds bibliographic metadata (DOI, authors, journal, year).

Reviewed changes

Copilot reviewed 68 out of 3596 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
H2_O2_NOx/Mathieu_2012/x10400008.yaml	Adds ignition delay shock-tube dataset (Mathieu 2012)
H2_O2_NOx/Mathieu_2012/x10400007.yaml	Adds ignition delay shock-tube dataset (Mathieu 2012)
H2_O2_NOx/Mathieu_2012/x10400006.yaml	Adds ignition delay shock-tube dataset (Mathieu 2012)
H2_O2_NOx/Mathieu_2012/x10400005.yaml	Adds ignition delay shock-tube dataset (Mathieu 2012)
H2_O2_NOx/Martin_1990/x60400017.yaml	Adds burner-stabilized flame speciation dataset (Martin 1990)
H2_O2_NOx/Martin_1990/x60400016.yaml	Adds burner-stabilized flame speciation dataset (Martin 1990)
H2_O2_NOx/Martin_1990/x60400015.yaml	Adds burner-stabilized flame speciation dataset (Martin 1990)
H2_O2_NOx/Martin_1990/x60200018.yaml	Adds burner-stabilized flame speciation dataset (Martin 1990)
H2_O2_NOx/Martin_1990/x60200017.yaml	Adds burner-stabilized flame speciation dataset (Martin 1990)
H2_O2_NOx/Martin_1990/x60200016.yaml	Adds burner-stabilized flame speciation dataset (Martin 1990)
H2_O2_NOx/Mainiero_1980/x60200041.yaml	Adds burner-stabilized flame speciation dataset (Mainiero 1980)
H2_O2_NOx/Mainiero_1980/x60200040.yaml	Adds burner-stabilized flame speciation dataset (Mainiero 1980)
H2_O2_NOx/Mainiero_1980/x60200039.yaml	Adds burner-stabilized flame speciation dataset (Mainiero 1980)
H2_O2_NOx/Löffler_2000/x30400016.yaml	Adds flow-reactor outlet concentration dataset (Löffler 2000)
H2_O2_NOx/Löffler_2000/x30400015.yaml	Adds flow-reactor outlet concentration dataset (Löffler 2000)
H2_O2_NOx/Kosarev_2007/x10400002.yaml	Adds ignition delay shock-tube dataset (Kosarev 2007)
H2_O2_NOx/Kosarev_2007/x10400001.yaml	Adds ignition delay shock-tube dataset (Kosarev 2007)
H2_O2_NOx/Hulgaard_1993/x30400006.yaml	Adds flow-reactor outlet concentration dataset (Hulgaard 1993)
H2_O2_NOx/Hulgaard_1993/x30400005.yaml	Adds flow-reactor outlet concentration dataset (Hulgaard 1993)
H2_O2_NOx/Hidaka_1985/x10400032.yaml	Adds ignition delay shock-tube dataset (Hidaka 1985)
H2_O2_NOx/Hidaka_1985/x10400029.yaml	Adds ignition delay shock-tube dataset (Hidaka 1985)
H2_O2_NOx/Henrici_1969/x10400060.yaml	Adds ignition delay shock-tube dataset (Henrici 1969)
H2_O2_NOx/Henrici_1969/x10400059.yaml	Adds ignition delay shock-tube dataset (Henrici 1969)
H2_O2_NOx/Henrici_1969/x10400058.yaml	Adds ignition delay shock-tube dataset (Henrici 1969)
H2_O2_NOx/Henrici_1969/x10400057.yaml	Adds ignition delay shock-tube dataset (Henrici 1969)
H2_O2_NOx/Dayma_2006/x00300002.yaml	Adds jet-stirred reactor dataset (Dayma 2006)
H2_O2_NOx/Dayma_2006/x00300001.yaml	Adds jet-stirred reactor dataset (Dayma 2006)
H2_O2_NOx/Dayma_2006/x00300000.yaml	Adds jet-stirred reactor dataset (Dayma 2006)
H2_O2_NOx/Dayma_2006/x00200008.yaml	Adds jet-stirred reactor dataset (Dayma 2006)
H2_O2_NOx/Dayma_2006/x00200004.yaml	Adds jet-stirred reactor dataset (Dayma 2006)
H2_O2_NOx/Bane_2011/x20400005.yaml	Adds laminar burning velocity dataset (Bane 2011)
H2_O2_NOx/Bane_2011/x20400004.yaml	Adds laminar burning velocity dataset (Bane 2011)
H2_O2_NOx/Bane_2011/x20400003.yaml	Adds laminar burning velocity dataset (Bane 2011)
H2_O2_NOx/Bane_2011/x20400002.yaml	Adds laminar burning velocity dataset (Bane 2011)
H2_O2_NOx/Bane_2011/x20400001.yaml	Adds laminar burning velocity dataset (Bane 2011)
H2_O2_NOx/Balakhnine_1977/x60400037.yaml	Adds burner-stabilized flame speciation dataset (Balakhnine 1977)
H2_O2_NOx/Balakhnine_1977/x60400036.yaml	Adds burner-stabilized flame speciation dataset (Balakhnine 1977)
H2_O2_NOx/Balakhnine_1977/x60400035.yaml	Adds burner-stabilized flame speciation dataset (Balakhnine 1977)
H2_O2_NOx/Balakhnine_1977/x60400034.yaml	Adds burner-stabilized flame speciation dataset (Balakhnine 1977)
H2_O2_NOx/Balakhnine_1977/x60400033.yaml	Adds burner-stabilized flame speciation dataset (Balakhnine 1977)
H2_O2_NOx/Balakhnine_1977/x60400031.yaml	Adds burner-stabilized flame speciation dataset (Balakhnine 1977)
H2_O2_NOx/Allen_1998/x30400003.yaml	Adds concentration time-profile dataset (Allen 1998)
H2_O2_NOx/Allen_1998/x30400002.yaml	Adds concentration time-profile dataset (Allen 1998)
H2_O2_NOx/Allen_1998/x30400001.yaml	Adds concentration time-profile dataset (Allen 1998)

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Copilot · 2026-03-28T01:35:09Z

+  temperature:
+  - 0700 K


Leading-zero numeric scalars (e.g., 0700) are risky in YAML because some parsers may interpret them as octal (or otherwise not as intended). Please remove the zero-padding (e.g., 700 K). This appears in multiple newly added datasets (temperatures/ignition-delays), so fixing at the conversion source would be preferable.

Copilot · 2026-03-28T01:35:10Z

+  - 023 us
+  pressure: *id001
+  composition: *id002
+  ignition-type: *id003
+- temperature:
+  - 1774 K
+  ignition-delay:
+  - 029 us
+  pressure: *id001
+  composition: *id002
+  ignition-type: *id003
+- temperature:
+  - 1735 K
+  ignition-delay:
+  - 031 us
+  pressure: *id001
+  composition: *id002
+  ignition-type: *id003
+- temperature:
+  - 1670 K
+  ignition-delay:
+  - 047 us
+  pressure: *id001
+  composition: *id002
+  ignition-type: *id003
+- temperature:
+  - 1613 K
+  ignition-delay:
+  - 089 us
+  pressure: *id001
+  composition: *id002
+  ignition-type: *id003
+- temperature:
+  - 1600 K
+  ignition-delay:
+  - 095 us


The ignition-delay value is zero-padded (023 us). Similar to temperature fields, this can be mis-parsed depending on YAML loader rules. Please emit unpadded values (e.g., 23 us) to avoid ambiguity and ensure correct numeric interpretation downstream.

Suggested change

- 023 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1774 K

ignition-delay:

- 029 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1735 K

ignition-delay:

- 031 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1670 K

ignition-delay:

- 047 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1613 K

ignition-delay:

- 089 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1600 K

ignition-delay:

- 095 us

- 23 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1774 K

ignition-delay:

- 29 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1735 K

ignition-delay:

- 31 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1670 K

ignition-delay:

- 47 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1613 K

ignition-delay:

- 89 us

pressure: *id001

composition: *id002

ignition-type: *id003

- temperature:

- 1600 K

ignition-delay:

- 95 us

Copilot · 2026-03-28T01:35:10Z

+    - species-name: H2
+      InChI: 1S/H2/h1H
+      amount:
+      - 0.101


This measured H2 mole fraction (0.101) is inconsistent with the experiment’s initial mixture in common-properties (H2 is 0.01). Given nearby files in the same study show ~0.01 at low temperatures, this looks like a decimal-place conversion error (likely 0.0101). Please verify against the source ReSpecTh/XML or publication and correct the datapoint (or the conversion logic) accordingly.

Suggested change

- 0.101

- 0.0101

Copilot · 2026-03-28T01:35:10Z

+reference:
+  doi: 10.1080/00102200600793171
+  authors:
+  - name: Guillame Dayma


Correct spelling of author given name from 'Guillame' to 'Guillaume'.

Suggested change

- name: Guillame Dayma

- name: Guillaume Dayma

Copilot · 2026-03-28T01:35:10Z

+    - species-name: H2
+      InChI: 1S/H2/h1H
+      amount:
+      - 0.00039999999999999996


Several numeric values have excessive floating-point expansion (e.g., 0.00039999999999999996). This makes the dataset noisy and increases diff churn without adding precision. Please round/format these to a reasonable number of significant digits (e.g., 0.0004) during conversion while staying consistent with the source data precision.

Suggested change

- 0.00039999999999999996

- 0.0004

… amounts

…dard formatting

…PyKED and PyTeCK

Re-ran batch_convert.py over all 3596 ReSpecTh/indirect XML files to apply accumulated fixes: corrected inverse unit notation (ms-1 → 1/ms), normalised page ranges (239--245 → 239-245), indented block sequences, removed non-schema fields, fixed d/dt min extrapolated ignition type, and improved author string parsing. 3585 files converted, 11 skipped, 0 errors.

Copilot

Pull request overview

Copilot reviewed 45 out of 3603 changed files in this pull request and generated 6 comments.

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Copilot · 2026-04-02T21:21:16Z

+reference:
+  doi: 10.1080/00102200600793171
+  authors:
+    - name: Guillame Dayma


The author first name appears misspelled as Guillame (commonly Guillaume). This impacts bibliographic metadata/searchability; please correct to the name as it appears in the publication and apply consistently across the Dayma_2006 converted files.

Suggested change

- name: Guillame Dayma

- name: Guillaume Dayma

Copilot · 2026-04-02T21:21:17Z

+comments:
+  - The inlet gas temperature is assumed to be room temperature (300 K) based on the
+    reported temperature profiles, experimental setup and other work of the authors
+    but any clear reference cannot be find for that


Grammar issue in the comment: cannot be find should be cannot be found.

Suggested change

but any clear reference cannot be find for that

but any clear reference cannot be found for that

Copilot · 2026-04-02T21:21:17Z

+        InChI: 1S/H2/h1H
+        amount:
+          - 0.01
+          - evaluated-standard-deviation: 0.0101


The evaluated standard deviation for the inlet H2 mole fraction (0.0101) is larger than the mean value (0.01), which is usually a strong indicator of a decimal/units transcription error. Please verify against the source and correct (e.g., 0.00101) if appropriate.

Suggested change

- evaluated-standard-deviation: 0.0101

- evaluated-standard-deviation: 0.00101

Copilot · 2026-04-02T21:21:17Z

+        - species-name: H2
+          InChI: 1S/H2/h1H
+          amount:
+            - 0.101


This measured H2 mole fraction (0.101) is ~10× larger than the stated inlet H2 mole fraction in common-properties (0.01). In a JSR oxidation experiment without an H-containing source besides H2, H2 should not increase above its inlet value. This looks like a likely decimal shift (0.0101). Please cross-check the original ReSpecTh XML / publication and correct the value if needed.

Suggested change

- 0.101

- 0.0101

Copilot · 2026-04-02T21:21:17Z

+            -- '*.yaml' '*.yml' \
+            | grep -v '^\.' \
+            | grep -v 'environment' \
+            | grep -v '.github/' \


The pattern passed to grep -v is a regular expression; .github/ matches any character + github/, not a literal .github/ directory. This can unintentionally exclude paths like xgithub/.... Use an anchored, escaped pattern (e.g., grep -vE '^\\.github/') to filter only the .github/ directory.

Suggested change

| grep -v '.github/' \

| grep -vE '^\\.github/' \

Copilot · 2026-04-02T21:21:18Z

+
+## Checklist
+
+- [ ] File has at least one `file-author` with a valid ORCID


The field name in ChemKED YAML is file-authors (plural), not file-author. Updating this will avoid confusion and aligns the template with the actual schema/keys used in the contributed YAML files.

Suggested change

- [ ] File has at least one `file-author` with a valid ORCID

- [ ] File has at least one `file-authors` entry with a valid ORCID

…tration type

…type

kyleniemeyer · 2026-04-03T22:28:26Z

@LekiaAnonim do we have any steps in place to check that our database does not already have a given dataset? I can imagine there might be some overlap in our existing database with the ReSpecTh database.

LekiaAnonim · 2026-04-04T14:24:34Z

@LekiaAnonim do we have any steps in place to check that our database does not already have a given dataset? I can imagine there might be some overlap in our existing database with the ReSpecTh database.

What it currently does is to check what directory to put a file. I will also make it check for duplicate contributions/content. I believe I only did that for the Website database. The goal was to treat duplicate contribution as a file change if it detects file diff and not to reject. But if the content agrees 100% or a review can be given by the maintainers. I can improve on this.

- Expanded journal abbreviations to full CrossRef titles - Fixed HTML entities in journal names (& not &) - Added author name formatting with periods in initials - Removed deprecated file-type field - Normalized YAML indentation and page number hyphens - Added uncertainty data where available from XML source

kyleniemeyer · 2026-04-06T17:13:52Z

@LekiaAnonim perhaps the check can be based on the source publication, since the DOI may be the easiest thing to check for duplication and flagging.

LekiaAnonim · 2026-04-06T23:17:54Z

@LekiaAnonim perhaps the check can be based on the source publication, since the DOI may be the easiest thing to check for duplication and flagging.

That was what I have done now, and added additional attributes to form a more holistic fingerprint for the data. The user can now view file disparity before they contribute, if duplicates are detected.

…rrected reference data to match Crossref suggestions

Added the latest version 2.3 and 2.4 of ReSpecTh data

4b83ca2

Copilot AI review requested due to automatic review settings March 28, 2026 01:33

Copilot AI reviewed Mar 28, 2026

View reviewed changes

LekiaAnonim added 7 commits March 27, 2026 23:25

fix: re-generate YAML files with corrected unit handling

44a685b

Regenerate YAML files with full property coverage in ReSpecTh

edf7188

regenerate YAML with inline uncertainty on properties and composition…

089ad23

… amounts

regenerate YAML with equivalence-ratio units, flow-style values, stan…

ce0a374

…dard formatting

Added GitHub actions for PR creation, and scripts for running CI for …

54722f1

…PyKED and PyTeCK

Fix validate_chemked.py to handle kdetermination/tdetermination files

cfa4ff5

LekiaAnonim force-pushed the Prosper_WIP branch from 2e04d41 to 2254ab3 Compare April 2, 2026 20:56

LekiaAnonim requested review from Copilot, kyleniemeyer and rwest April 2, 2026 21:10

Copilot AI reviewed Apr 2, 2026

View reviewed changes

LekiaAnonim added 2 commits April 2, 2026 18:58

Regenerate YAMLs: fix ignition target semicolons, add relative concen…

e1ef300

…tration type

Regenerate YAMLs: capture amount for relative concentration ignition …

6741807

…type

LekiaAnonim added 2 commits April 5, 2026 15:28

Add 133 new datasets from ReSpecTh batch conversion

4365c9a

Re-converted ReSpecTh data to capture multiple apparatus mode, And co…

a75baac

…rrected reference data to match Crossref suggestions

	but any clear reference cannot be find for that
	but any clear reference cannot be found for that

	- evaluated-standard-deviation: 0.0101
	- evaluated-standard-deviation: 0.00101


		## Checklist

		- [ ] File has at least one `file-author` with a valid ORCID

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kyleniemeyer commented Apr 3, 2026

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LekiaAnonim commented Apr 4, 2026 •

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