ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database

Removed database entries

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#133 8 comments 0 reactions 0 assignees View on GitHub

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Python
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Description

I'm writing this issue as a place to store entries removed from RMG-database. Sometimes changes in code or questionable sources may make us want to remove some (hopefully temporarily). Putting them here, prevents them from being lost forever, especially if they are unpublished or unrecorded elsewhere.

The following entry was removed because we recently changed out Nitrogen atomtypes to be more specific. Previously it was 'swept under the rug', probably falling under some atomtype that was not intended. In the current working version of NAtomType branch, there is no atomtype to describe the negative 2 charged nitrogen:

from thermo_DFT_CCSDTF12_BAC thermo library:

entry(
index = 434,
label = "NNH2(S)",
molecule =
"""
1 N u0 p0 c+2 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 N u0 p3 c-2 {1,S}
""",
thermo = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],'K'),
Cpdata = ([8.61,9.45,10.46,11.48,13.24,14.63,16.86],'cal/(molK)'),
H298 = (71.66,'kcal/mol'),
S298 = (52.09,'cal/(mol
K)'),
),
shortDesc = u"""""",
longDesc =
u"""
level of theory: CCSD(T)F12A/cc-pVTZ-F12//B3LYP/6-311++g(d,p) + BAC
""",
)

Edit: The above entry is now re-implemented with #163.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Read the archived entry in this issue and follow the reference to #163, which states that the entry was re-implemented. Confirm that no further database change is requested; the issue serves as a record of removed RMG-database content rather than an open implementation task.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
databases
Issue type
Documentation
Difficulty
1/5
Estimated time
Under an hour
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
10/100

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