ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

Cannot compute rates if a reactants/product species is given from an Arkane YAML file

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Type: Bug
Dominant language
Python
Stars
51
Forks
25
Avg merge
4d 5h
Merged PRs (30d)
15

Description

Describe the bug
We gave the following input:

project: xh2010

level_of_theory: cbs-qb3
compute_thermo: false
freq_scale_factor: 1
job_types:
  rotors: false 
species:
  - label: N2H3 #N2H3(14)
    multiplicity: 2
    smiles: N[NH]
    yml_path: /N2H3.yml
  - label: HNNH_S #N2H2(16)
    adjlist: | 
             1 N u0 p1 c0 {2,D} {3,S}
             2 N u0 p1 c0 {1,D} {4,S}
             3 H u0 p0 c0 {1,S}
             4 H u0 p0 c0 {2,S}
  - label: H2NN_S #N2H2(18)
    adjlist: | 
             1 N u0 p0 c+1 {2,D} {3,S} {4,S}
             2 N u0 p2 c-1 {1,D}
             3 H u0 p0 c0 {1,S}
             4 H u0 p0 c0 {1,S}
  - label: NNH_T #NNH(71)
    multiplicity: 2
    adjlist: |
             1 N u0 p1 c0 {2,D} {3,S}
             2 N u1 p1 c0 {1,D}
             3 H u0 p0 c0 {1,S}

reactions:
  - label: N2H3 + NNH_T <=> HNNH_S + HNNH_S
    ts_xyz_guess: 
    - TS5_1.xyz

TS5_1.xyz:

8
TS5_1 optimized at cbs-qb3
N      -0.68300700    0.03920500   -0.01784800
N       0.59224500    0.17784500   -0.25555500
H      -1.15241800   -0.11589500   -0.91590900
H      -1.11625500    1.05983800    0.37745200
H       1.04909600    0.28531300    0.65574300
N       0.28393500    2.40293300   -0.02808700
N      -0.86072400    2.47720000    0.28870900
H       0.81945200    3.28758400   -0.10802200

N2H3.yml:

RMG_version: 3.1.0
adjacency_list: |
  multiplicity 2
  1 N u0 p1 c0 {2,S} {3,S} {4,S}
  2 N u1 p1 c0 {1,S} {5,S}
  3 H u0 p0 c0 {1,S}
  4 H u0 p0 c0 {1,S}
  5 H u0 p0 c0 {2,S}
charge: 0
chemkin_thermo_string: |
  N2H3                    H   3N   2          G    10.000  3000.000  350.19      1
   2.24346053E+00 1.16909712E-02-6.10437318E-06 1.62082407E-09-1.71821013E-13    2
   2.45063257E+04 1.32073021E+01 4.04686435E+00-4.17784458E-03 4.16057334E-05    3
  -5.06318502E-08 9.59258103E-12 2.43510147E+04 5.98507052E+00                   4
class: ArkaneSpecies
conformer:
  E0:
    class: ScalarQuantity
    units: kJ/mol
    value: 202.4587661272151
  class: Conformer
  coordinates:
    class: ArrayQuantity
    units: angstroms
    value:
      class: np_array
      object:
      - - -0.423202
        - 0.0031879999999999994
        - 0.17559
      - - 0.791998
        - -0.531317
        - -0.089405
      - - -1.18531
        - -0.643555
        - 0.030107
      - - -0.637947
        - 0.959795
        - -0.089111
      - - 1.43929
        - 0.262891
        - -0.107737
  mass:
    class: ArrayQuantity
    units: amu
    value:
      class: np_array
      object:
      - 14.00307400443
      - 14.00307400443
      - 1.00782503224
      - 1.00782503224
      - 1.00782503224
  modes:
  - class: IdealGasTranslation
    mass:
      class: ScalarQuantity
      units: amu
      value: 31.029620000000005
    quantum: false
  - class: NonlinearRotor
    inertia:
      class: ArrayQuantity
      units: amu*angstrom^2
      value:
        class: np_array
        object:
        - 2.4805399332066242
        - 16.541888316394743
        - 18.72298334799242
    quantum: false
    rotationalConstant:
      class: ArrayQuantity
      units: cm^-1
      value:
        class: np_array
        object:
        - 6.79595148930194
        - 1.0190873454659235
        - 0.9003708832094891
    symmetry: 1
  - class: HarmonicOscillator
    frequencies:
      class: ArrayQuantity
      units: cm^-1
      value:
        class: np_array
        object:
        - 580.190604816537
        - 714.8648764077677
        - 1146.2104788486065
        - 1239.4121636437396
        - 1495.3923561698548
        - 1675.5999557273262
        - 3410.610927028133
        - 3480.194727182487
        - 3633.6656254272652
    quantum: true
  number:
    class: ArrayQuantity
    value:
      class: np_array
      object:
      - 7.0
      - 7.0
      - 1.0
      - 1.0
      - 1.0
  optical_isomers: 2
  spin_multiplicity: 2
datetime: 2022-05-30 17:39
formula: H3N2
inchi: InChI=1S/H3N2/c1-2/h1H,2H2
inchi_key: LURQBQNWDYASPJ-UHFFFAOYSA-N
is_ts: false
label: N2H3
molecular_weight:
  class: ScalarQuantity
  units: amu
  value: 31.03763485763127
multiplicity: 2
smiles: '[NH]N'
thermo:
  Cp0:
    class: ScalarQuantity
    units: J/(mol*K)
    value: 33.257888
  CpInf:
    class: ScalarQuantity
    units: J/(mol*K)
    value: 108.08813599999999
  E0:
    class: ScalarQuantity
    units: kJ/mol
    value: 202.46339830137327
  Tmax:
    class: ScalarQuantity
    units: K
    value: 3000.0
  Tmin:
    class: ScalarQuantity
    units: K
    value: 10.0
  class: NASA
  polynomials:
    polynomial1:
      Tmax:
        class: ScalarQuantity
        units: K
        value: 350.18692551807146
      Tmin:
        class: ScalarQuantity
        units: K
        value: 10.0
      class: NASAPolynomial
      coeffs:
        class: np_array
        object:
        - 4.046864353249508
        - -0.004177844580689019
        - 4.1605733369059456e-05
        - -5.063185015261333e-08
        - 9.592581033254738e-12
        - 24351.014666958064
        - 5.98507052402682
    polynomial2:
      Tmax:
        class: ScalarQuantity
        units: K
        value: 3000.0
      Tmin:
        class: ScalarQuantity
        units: K
        value: 350.18692551807146
      class: NASAPolynomial
      coeffs:
        class: np_array
        object:
        - 2.2434605251957467
        - 0.011690971222545773
        - -6.1043731811830374e-06
        - 1.6208240695555914e-09
        - -1.718210126371354e-13
        - 24506.325699213452
        - 13.207302056500666
thermo_data:
  Cpdata:
    class: ArrayQuantity
    units: cal/(mol*K)
    value:
      class: np_array
      object:
      - 10.430185053605145
      - 12.007662349549431
      - 13.423017607205214
      - 14.682075623534569
      - 16.78975412368534
      - 18.43941158094492
      - 21.154836732516408
      - 22.704562782939714
      - 23.54097490819626
  H298:
    class: ScalarQuantity
    units: kcal/mol
    value: 50.958282136896564
  S298:
    class: ScalarQuantity
    units: cal/(mol*K)
    value: 58.056424230772535
  Tdata:
    class: ArrayQuantity
    units: K
    value:
      class: np_array
      object:
      - 300.0
      - 400.0
      - 500.0
      - 600.0
      - 800.0
      - 1000.0
      - 1500.0
      - 2000.0
      - 2400.0
  class: ThermoData
xyz: |-
  5
  N2H3
  N      -0.42320200    0.00318800    0.17559000
  N       0.79199800   -0.53131700   -0.08940500
  H      -1.18531000   -0.64355500    0.03010700
  H      -0.63794700    0.95979500   -0.08911100
  H       1.43929000    0.26289100   -0.10773700

ARC did not compute any rate since it didn't get E0 for the N2H3 species tread from YAML:

Reaction N2H3 + NNH_T <=> HNNH_S + HNNH_S (TS TS0) has the following path electronic energy:
Reactants: None
TS: 64.83 kJ/mol
Products: 0.00 kJ/mol

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

Start by reproducing the issue with the provided ARC input and Arkane YAML, then trace how the species yml_path is loaded and how E0 values enter rate calculations. Done means the N2H3 reactant receives its YAML E0 and the reaction produces a computed rate instead of reporting Reactants: None.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, yaml
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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