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Inconsistent electronic states for atomic carbon #171

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rwest opened this issue Mar 17, 2017 · 3 comments
Closed
24 tasks done

Inconsistent electronic states for atomic carbon #171

rwest opened this issue Mar 17, 2017 · 3 comments

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@rwest
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rwest commented Mar 17, 2017 •
edited by alongd
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Running grep '1 *C *u[0-9] *p[0-9] *c[0-9] *$' -B4 -A1 -r . in the database shows a range of choices that have been made for the multiplicity and electronic structure of atomic carbon. In a couple of cases this has obviously been thought about , for example primaryThermoLibrary.py contains both

    label = "C(S)",
    molecule = 
"""
1 C u0 p2 c0
""",

and

    label = "C(T)",
    molecule = 
"""
multiplicity 3
1 C u2 p1 c0
""",

(the chosen labels make it clear that one was meant to be singlet and one triplet)
however, some of them appear to be auto-generated adjacency lists in the quintuplet state,
which is probably not right.

We should check each of these:

./kinetics/libraries/Dooley/C1/dictionary.txt-C
./kinetics/libraries/Dooley/C1/dictionary.txt-multiplicity 5
./kinetics/libraries/Dooley/C1/dictionary.txt:1 C u4 p0 c0
./kinetics/libraries/Dooley/C1/dictionary.txt-
--
--
./kinetics/libraries/Dooley/methylformate/dictionary.txt-C
./kinetics/libraries/Dooley/methylformate/dictionary.txt-multiplicity 5
./kinetics/libraries/Dooley/methylformate/dictionary.txt:1 C u4 p0 c0
./kinetics/libraries/Dooley/methylformate/dictionary.txt-
--
--
./kinetics/libraries/Dooley/methylformate_all_ARHEbathgas/dictionary.txt-C
./kinetics/libraries/Dooley/methylformate_all_ARHEbathgas/dictionary.txt-multiplicity 5
./kinetics/libraries/Dooley/methylformate_all_ARHEbathgas/dictionary.txt:1 C u4 p0 c0
./kinetics/libraries/Dooley/methylformate_all_ARHEbathgas/dictionary.txt-
--
--
./kinetics/libraries/Dooley/methylformate_all_N2bathgas/dictionary.txt-C
./kinetics/libraries/Dooley/methylformate_all_N2bathgas/dictionary.txt-multiplicity 5
./kinetics/libraries/Dooley/methylformate_all_N2bathgas/dictionary.txt:1 C u4 p0 c0
./kinetics/libraries/Dooley/methylformate_all_N2bathgas/dictionary.txt-
--
--
./kinetics/libraries/ERC-FoundationFuelv0.9/dictionary.txt-C(T)
./kinetics/libraries/ERC-FoundationFuelv0.9/dictionary.txt-multiplicity 3
./kinetics/libraries/ERC-FoundationFuelv0.9/dictionary.txt:1 C u2 p1 c0
--
--
./kinetics/libraries/FFCM1(-)/dictionary.txt-C
./kinetics/libraries/FFCM1(-)/dictionary.txt-multiplicity 5
./kinetics/libraries/FFCM1(-)/dictionary.txt:1 C u4 p0 c0
--
--
./kinetics/libraries/GRI-Mech3.0/dictionary.txt-C
./kinetics/libraries/GRI-Mech3.0/dictionary.txt-multiplicity 3
./kinetics/libraries/GRI-Mech3.0/dictionary.txt:1 C u2 p1 c0
--
--
./kinetics/libraries/GRI-Mech3.0-N/dictionary.txt-C(T)
./kinetics/libraries/GRI-Mech3.0-N/dictionary.txt-multiplicity 3
./kinetics/libraries/GRI-Mech3.0-N/dictionary.txt:1 C u2 p1 c0
--
--
./kinetics/libraries/JetSurF0.2/dictionary.txt-C
./kinetics/libraries/JetSurF0.2/dictionary.txt-multiplicity 5
./kinetics/libraries/JetSurF0.2/dictionary.txt:1 C u4 p0 c0
--
--
./kinetics/libraries/Nitrogen_Dean_and_Bozzelli/dictionary.txt-C(T)
./kinetics/libraries/Nitrogen_Dean_and_Bozzelli/dictionary.txt-multiplicity 3
./kinetics/libraries/Nitrogen_Dean_and_Bozzelli/dictionary.txt:1 C u2 p1 c0
--
--
./kinetics/libraries/Nitrogen_Glarborg_Gimenez_et_al/dictionary.txt-C(T)
./kinetics/libraries/Nitrogen_Glarborg_Gimenez_et_al/dictionary.txt-multiplicity 3
./kinetics/libraries/Nitrogen_Glarborg_Gimenez_et_al/dictionary.txt:1 C u2 p1 c0
--
--
./kinetics/libraries/Nitrogen_Glarborg_Zhang_et_al/dictionary.txt-C(T)
./kinetics/libraries/Nitrogen_Glarborg_Zhang_et_al/dictionary.txt-multiplicity 3
./kinetics/libraries/Nitrogen_Glarborg_Zhang_et_al/dictionary.txt:1 C u2 p1 c0
--
--
./thermo/libraries/Chernov.py-    label = "C",
./thermo/libraries/Chernov.py-    molecule = 
./thermo/libraries/Chernov.py-"""
./thermo/libraries/Chernov.py:1 C u0 p2 c0
./thermo/libraries/Chernov.py-""",
--
--
./thermo/libraries/FFCM1(-).py-    label = "C",
./thermo/libraries/FFCM1(-).py-    molecule = 
./thermo/libraries/FFCM1(-).py-"""
./thermo/libraries/FFCM1(-).py-multiplicity 5
./thermo/libraries/FFCM1(-).py:1 C u4 p0 c0
./thermo/libraries/FFCM1(-).py-""",
--
--
./thermo/libraries/GRI-Mech3.0-N.py-    label = "C(T)",
./thermo/libraries/GRI-Mech3.0-N.py-    molecule = 
./thermo/libraries/GRI-Mech3.0-N.py-"""
./thermo/libraries/GRI-Mech3.0-N.py-multiplicity 3
./thermo/libraries/GRI-Mech3.0-N.py:1 C u2 p1 c0
./thermo/libraries/GRI-Mech3.0-N.py-""",
--
--
./thermo/libraries/GRI-Mech3.0.py-    label = "C(T)",
./thermo/libraries/GRI-Mech3.0.py-    molecule = 
./thermo/libraries/GRI-Mech3.0.py-"""
./thermo/libraries/GRI-Mech3.0.py-multiplicity 3
./thermo/libraries/GRI-Mech3.0.py:1 C u2 p1 c0
./thermo/libraries/GRI-Mech3.0.py-""",
--
--
./thermo/libraries/JetSurF0.2.py-    label = "C",
./thermo/libraries/JetSurF0.2.py-    molecule = 
./thermo/libraries/JetSurF0.2.py-"""
./thermo/libraries/JetSurF0.2.py-multiplicity 5
./thermo/libraries/JetSurF0.2.py:1 C u4 p0 c0
./thermo/libraries/JetSurF0.2.py-""",
--
--
./thermo/libraries/Narayanaswamy.py-    label = "C(13)",
./thermo/libraries/Narayanaswamy.py-    molecule = 
./thermo/libraries/Narayanaswamy.py-"""
./thermo/libraries/Narayanaswamy.py:1 C u0 p2 c0
./thermo/libraries/Narayanaswamy.py-""",
--
--
./thermo/libraries/NISTThermoLibrary.py-    label = "C(T)",
./thermo/libraries/NISTThermoLibrary.py-    molecule = 
./thermo/libraries/NISTThermoLibrary.py-"""
./thermo/libraries/NISTThermoLibrary.py-multiplicity 3
./thermo/libraries/NISTThermoLibrary.py:1 C u2 p1 c0
./thermo/libraries/NISTThermoLibrary.py-""",
--
--
./thermo/libraries/primaryThermoLibrary.py-    label = "C(S)",
./thermo/libraries/primaryThermoLibrary.py-    molecule = 
./thermo/libraries/primaryThermoLibrary.py-"""
./thermo/libraries/primaryThermoLibrary.py:1 C u0 p2 c0
./thermo/libraries/primaryThermoLibrary.py-""",
--
--
./thermo/libraries/primaryThermoLibrary.py-    label = "C(T)",
./thermo/libraries/primaryThermoLibrary.py-    molecule = 
./thermo/libraries/primaryThermoLibrary.py-"""
./thermo/libraries/primaryThermoLibrary.py-multiplicity 3
./thermo/libraries/primaryThermoLibrary.py:1 C u2 p1 c0
./thermo/libraries/primaryThermoLibrary.py-""",
--
--
./thermo/libraries/USC-Mech-ii.py-    label = "C(T)",
./thermo/libraries/USC-Mech-ii.py-    molecule = 
./thermo/libraries/USC-Mech-ii.py-"""
./thermo/libraries/USC-Mech-ii.py-multiplicity 3
./thermo/libraries/USC-Mech-ii.py:1 C u2 p1 c0
./thermo/libraries/USC-Mech-ii.py-""",
--
--
./transport/libraries/GRI-Mech.py-    label = "C(T)",
./transport/libraries/GRI-Mech.py-    molecule = 
./transport/libraries/GRI-Mech.py-"""
./transport/libraries/GRI-Mech.py-multiplicity 3
./transport/libraries/GRI-Mech.py:1 C u2 p1 c0
./transport/libraries/GRI-Mech.py-""",
--
--
./transport/libraries/PrimaryTransportLibrary.py-    label = "C(S)",
./transport/libraries/PrimaryTransportLibrary.py-    molecule = 
./transport/libraries/PrimaryTransportLibrary.py-"""
./transport/libraries/PrimaryTransportLibrary.py:1 C u0 p2 c0
./transport/libraries/PrimaryTransportLibrary.py-""",

(Also, the SMILES interpretation and generation is broken for these, but that's an RMG-Py issue that I'll open later)

Check these off when checked (or corrected):

  • kinetics/libraries/Dooley/C1/dictionary.txt:1 C u4 p0 c0
  • kinetics/libraries/Dooley/methylformate/dictionary.txt:1 C u4 p0 c0
  • kinetics/libraries/Dooley/methylformate_all_ARHEbathgas/dictionary.txt:1 C u4 p0 c0
  • kinetics/libraries/Dooley/methylformate_all_N2bathgas/dictionary.txt:1 C u4 p0 c0
  • kinetics/libraries/ERC-FoundationFuelv0.9/dictionary.txt:1 C u2 p1 c0
  • kinetics/libraries/FFCM1(-)/dictionary.txt:1 C u4 p0 c0
  • kinetics/libraries/GRI-Mech3.0/dictionary.txt:1 C u2 p1 c0
  • kinetics/libraries/GRI-Mech3.0-N/dictionary.txt:1 C u2 p1 c0
  • kinetics/libraries/JetSurF0.2/dictionary.txt:1 C u4 p0 c0
  • kinetics/libraries/Nitrogen_Dean_and_Bozzelli/dictionary.txt:1 C u2 p1 c0
  • kinetics/libraries/Nitrogen_Glarborg_Gimenez_et_al/dictionary.txt:1 C u2 p1 c0
  • kinetics/libraries/Nitrogen_Glarborg_Zhang_et_al/dictionary.txt:1 C u2 p1 c0
  • thermo/libraries/Chernov.py:1 C u0 p2 c0
  • thermo/libraries/FFCM1(-).py:1 C u4 p0 c0
  • thermo/libraries/GRI-Mech3.0-N.py:1 C u2 p1 c0
  • thermo/libraries/GRI-Mech3.0.py:1 C u2 p1 c0
  • thermo/libraries/JetSurF0.2.py:1 C u4 p0 c0
  • thermo/libraries/Narayanaswamy.py:1 C u0 p2 c0
  • thermo/libraries/NISTThermoLibrary.py:1 C u2 p1 c0
  • thermo/libraries/primaryThermoLibrary.py:1 C u0 p2 c0
  • thermo/libraries/primaryThermoLibrary.py:1 C u2 p1 c0
  • thermo/libraries/USC-Mech-ii.py:1 C u2 p1 c0
  • transport/libraries/GRI-Mech.py:1 C u2 p1 c0
  • transport/libraries/PrimaryTransportLibrary.py:1 C u0 p2 c0
This was referenced Mar 18, 2017
Closed
Closed
This was referenced Mar 21, 2017
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Open
alongd added a commit that referenced this issue Mar 24, 2017
@alongd
The JetSurF libraries were corrected for [C], [CH], [CH2], [OH]
2555aef 
Originally I mistakenly naked these libraries `0.2`, where infact they are version `2.0`.
The libraries names were corrected now as well.

Main changes in this commit are:
- The AdjLists of [C] were corrected to a multiplicity 3 instead of 5 (see issue #171)
- The AdjLists of [CH] were corrected to a multiplicity 2 instead of 4 (see issue #172)
- THe representation of CH2 and CH2(S) was correct and wasn't changed
alongd added a commit that referenced this issue Mar 24, 2017
@alongd
The JetSurF libraries were corrected for [C], [CH], [CH2], [OH]
38902d1 
Originally I mistakenly naked these libraries `0.2`, where infact they are version `2.0`.
The libraries names were corrected now as well.

Main changes in this commit are:
- The AdjLists of [C] were corrected to a multiplicity 3 instead of 5 (see issue #171)
- The AdjLists of [CH] were corrected to a multiplicity 2 instead of 4 (see issue #172)
- The representation of CH2 and CH2(S) was correct and wasn't changed
- Reactions of `[CH]*` and `[OH]*` (which currently cannot be represented in RMG) were added as a comment
alongd added a commit that referenced this issue Mar 24, 2017
@alongd
The JetSurF libraries were corrected for [C], [CH], [CH2], [OH]
37a61ef 
Originally I mistakenly named these libraries `0.2`, where infact they are version `2.0`.
The libraries names were corrected now as well.

Main changes in this commit are:
- The AdjLists of [C] were corrected to a multiplicity 3 instead of 5 (see issue #171)
- The AdjLists of [CH] were corrected to a multiplicity 2 instead of 4 (see issue #172)
- The representation of CH2 and CH2(S) was correct and wasn't changed
- Reactions of `[CH]*` and `[OH]*` (which currently cannot be represented in RMG) were added as a comment
@alongd alongd mentioned this issue Mar 24, 2017
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@alongd
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alongd commented Mar 27, 2017

I think this can be closed after #180 is merged.

@rwest
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rwest commented Mar 27, 2017

Thanks Alon!

@KEHANG
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KEHANG commented Mar 28, 2017

fixed by #180

@KEHANG KEHANG closed this as completed Mar 28, 2017
mliu49 pushed a commit to mliu49/RMG-database that referenced this issue Mar 29, 2017
@alongd @mliu49
The JetSurF libraries were corrected for [C], [CH], [CH2], [OH]
e2f6dcf 
Originally I mistakenly named these libraries `0.2`, where infact they are version `2.0`.
The libraries names were corrected now as well.

Main changes in this commit are:
- The AdjLists of [C] were corrected to a multiplicity 3 instead of 5 (see issue ReactionMechanismGenerator#171)
- The AdjLists of [CH] were corrected to a multiplicity 2 instead of 4 (see issue ReactionMechanismGenerator#172)
- The representation of CH2 and CH2(S) was correct and wasn't changed
- Reactions of `[CH]*` and `[OH]*` (which currently cannot be represented in RMG) were added as a comment
alongd added a commit to alongd/RMG-database that referenced this issue Aug 23, 2017
@alongd
The JetSurF libraries were corrected for [C], [CH], [CH2], [OH]
b6a1f76 
Originally I mistakenly named these libraries `0.2`, where infact they are version `2.0`.
The libraries names were corrected now as well.

Main changes in this commit are:
- The AdjLists of [C] were corrected to a multiplicity 3 instead of 5 (see issue ReactionMechanismGenerator#171)
- The AdjLists of [CH] were corrected to a multiplicity 2 instead of 4 (see issue ReactionMechanismGenerator#172)
- The representation of CH2 and CH2(S) was correct and wasn't changed
- Reactions of `[CH]*` and `[OH]*` (which currently cannot be represented in RMG) were added as a comment
goldmanm pushed a commit that referenced this issue Aug 24, 2017
@alongd @goldmanm
The JetSurF libraries were corrected for [C], [CH], [CH2], [OH]
3a4ba03 
Originally I mistakenly named these libraries `0.2`, where infact they are version `2.0`.
The libraries names were corrected now as well.

Main changes in this commit are:
- The AdjLists of [C] were corrected to a multiplicity 3 instead of 5 (see issue #171)
- The AdjLists of [CH] were corrected to a multiplicity 2 instead of 4 (see issue #172)
- The representation of CH2 and CH2(S) was correct and wasn't changed
- Reactions of `[CH]*` and `[OH]*` (which currently cannot be represented in RMG) were added as a comment
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@rwest @KEHANG @alongd