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Merge pull request #2065 from ReactionMechanismGenerator/cse
BigFix: Correct indices in me.pyx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| #!/usr/bin/env python3 | ||
| # encoding: utf-8 | ||
|
|
||
| title = 'CH2NH2 PES' | ||
| description = """ | ||
| Calculations done using ARC at the following levels of theory: | ||
| opt: wb97xd/6-311++g(d,p) | ||
| freq: wb97xd/6-311++g(d,p) | ||
| sp: ccsd(t)-f12/cc-pvqz-f12 | ||
| 1D rotor scans: wb97xd/6-311++g(d,p) | ||
| """ | ||
|
|
||
| modelChemistry = "CCSD(T)-F12/cc-pvqz-f12" | ||
|
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||
| useHinderedRotors = True | ||
| useBondCorrections = False | ||
|
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|
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| species('CH2NH2', 'yaml_files/CH2NH2.yml', | ||
| collisionModel = TransportData(sigma=(3.626,'angstrom'), epsilon=(481.8,'J/mol')), | ||
| energyTransferModel = SingleExponentialDown(alpha0=(133,'cm^-1'), T0=(300,'K'), n=0.85), # C3H4/N2 | ||
| ) | ||
|
|
||
| species('CH3NH', 'yaml_files/CH3NH.yml', | ||
| collisionModel = TransportData(sigma=(3.626,'angstrom'), epsilon=(481.8,'J/mol')), | ||
| energyTransferModel = SingleExponentialDown(alpha0=(133,'cm^-1'), T0=(300,'K'), n=0.85), # C3H4/N2 | ||
| ) | ||
|
|
||
| species('CH2NH', 'yaml_files/CH2NH.yml', | ||
| collisionModel = TransportData(sigma=(3.690,'angstrom'), epsilon=(417.0,'J/mol')), | ||
| energyTransferModel = SingleExponentialDown(alpha0=(133,'cm^-1'), T0=(300,'K'), n=0.85), # C3H4/N2 | ||
| ) | ||
|
|
||
| species('H', 'yaml_files/H.yml', | ||
| collisionModel = TransportData(sigma=(2.050,'angstrom'), epsilon=(145.0,'J/mol')), | ||
| energyTransferModel = SingleExponentialDown(alpha0=(133,'cm^-1'), T0=(300,'K'), n=0.85), # C3H4/N2 | ||
| ) | ||
|
|
||
| species( | ||
| label = 'Ar', | ||
| structure = SMILES('[Ar]'), | ||
| E0 = (-6.19426,'kJ/mol'), | ||
| spinMultiplicity = 1, | ||
| opticalIsomers = 1, | ||
| molecularWeight = (39.348,'amu'), | ||
| collisionModel = TransportData(shapeIndex=0, epsilon=(1134.93,'J/mol'), sigma=(3.33,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0.0, comment="""GRI-Mech"""), | ||
| energyTransferModel = SingleExponentialDown(alpha0=(133,'cm^-1'), T0=(300,'K'), n=0.85), | ||
| thermo = NASA(polynomials=[NASAPolynomial(coeffs=[2.5,2.64613e-14,-3.72536e-17,1.7192e-20,-2.44483e-24,-745,4.3663], Tmin=(100,'K'), Tmax=(3802.52,'K')), NASAPolynomial(coeffs=[2.5,1.04239e-10,-3.81845e-14,6.18592e-18,-3.73869e-22,-745,4.3663], Tmin=(3802.52,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-6.19426,'kJ/mol'), Cp0=(20.7862,'J/(mol*K)'), CpInf=(20.7862,'J/(mol*K)'), label="""Ar""", comment="""Thermo library: BurkeH2O2"""), | ||
| ) | ||
|
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||
| transitionState('CH2NH_to_CH2NH2','yaml_files/CH2NH_to_CH2NH2.yml') | ||
|
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| transitionState('CH2NH_to_CH3NH','yaml_files/CH2NH_to_CH3NH.yml') | ||
|
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| transitionState('CH3NH_to_CH2NH2','yaml_files/CH3NH_to_CH2NH2.yml') | ||
|
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||
| reaction( | ||
| label = 'CH3NH = CH2NH2', | ||
| reactants = ['CH3NH'], | ||
| products = ['CH2NH2'], | ||
| transitionState = 'CH3NH_to_CH2NH2', | ||
| tunneling = 'Eckart', | ||
| ) | ||
|
|
||
| reaction( | ||
| label = 'CH2NH + H = CH2NH2', | ||
| reactants = ['CH2NH', 'H'], | ||
| products = ['CH2NH2'], | ||
| transitionState = 'CH2NH_to_CH2NH2', | ||
| tunneling = 'Eckart', | ||
| ) | ||
|
|
||
| reaction( | ||
| label = 'CH2NH + H = CH3NH', | ||
| reactants = ['CH2NH', 'H'], | ||
| products = ['CH3NH'], | ||
| transitionState = 'CH2NH_to_CH3NH', | ||
| tunneling = 'Eckart', | ||
| ) | ||
|
|
||
| network( | ||
| label = 'CH2NH2', | ||
| isomers = ['CH2NH2', 'CH3NH'], | ||
| reactants = [('CH2NH', 'H')], | ||
| bathGas = {'Ar': 1} | ||
| ) | ||
|
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||
| pressureDependence( | ||
| label='CH2NH2', | ||
| Tmin=(500.0,'K'), Tmax=(2500.0,'K'), Tcount=25, | ||
| Pmin=(0.01,'bar'), Pmax=(100.0,'bar'), Pcount=15, | ||
| maximumGrainSize = (0.5,'kcal/mol'), | ||
| minimumGrainCount = 250, | ||
| method = 'chemically-significant eigenvalues', # use the CSE method which is more expensive, less robust, yet more accurate, see: http://reactionmechanismgenerator.github.io/RMG-Py/theory/pdep/methods.html#the-chemically-signficant-eigenvalues-method | ||
| interpolationModel = ('chebyshev', 6, 4), | ||
| activeKRotor = True, | ||
| activeJRotor = True, | ||
| ) |
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| @@ -0,0 +1,245 @@ | ||
| RMG_version: 3.0.0 | ||
| adjacency_list: | | ||
| 1 N u0 p1 c0 {2,D} {5,S} | ||
| 2 C u0 p0 c0 {1,D} {3,S} {4,S} | ||
| 3 H u0 p0 c0 {2,S} | ||
| 4 H u0 p0 c0 {2,S} | ||
| 5 H u0 p0 c0 {1,S} | ||
| author: Duminda Ranasinghe | ||
| chemkin_thermo_string: | | ||
| CH2NH_GS C 1H 3N 1 G 10.000 3000.000 929.04 1 | ||
| 8.90142813E-01 1.36790591E-02-6.97921272E-06 1.73897882E-09-1.70110463E-13 2 | ||
| 1.12137680E+04 1.84259478E+01 4.08222115E+00-4.85090203E-03 3.06667703E-05 3 | ||
| -3.08208892E-08 1.00838992E-11 1.08272132E+04 4.37264781E+00 4 | ||
| class: ArkaneSpecies | ||
| conformer: | ||
| E0: | ||
| class: ScalarQuantity | ||
| units: kJ/mol | ||
| value: 89.98686934415784 | ||
| class: Conformer | ||
| coordinates: | ||
| class: ArrayQuantity | ||
| units: angstroms | ||
| value: | ||
| class: np_array | ||
| object: | ||
| - - 0.5848679999999999 | ||
| - 0.028840999999999995 | ||
| - -1.3e-05 | ||
| - - 1.07168 | ||
| - 1.010862 | ||
| - -1.1999999999999999e-05 | ||
| - - 1.243754 | ||
| - -0.840878 | ||
| - -1.8e-05 | ||
| - - -0.665934 | ||
| - -0.154335 | ||
| - -1.0e-05 | ||
| - - -1.163388 | ||
| - 0.737184 | ||
| - -5.999999999999999e-06 | ||
| mass: | ||
| class: ArrayQuantity | ||
| units: amu | ||
| value: | ||
| class: np_array | ||
| object: | ||
| - 12.000000000000002 | ||
| - 1.00782503224 | ||
| - 1.00782503224 | ||
| - 14.00307400443 | ||
| - 1.00782503224 | ||
| modes: | ||
| - class: IdealGasTranslation | ||
| mass: | ||
| class: ScalarQuantity | ||
| units: amu | ||
| value: 29.026550000000004 | ||
| quantum: false | ||
| - class: NonlinearRotor | ||
| inertia: | ||
| class: ArrayQuantity | ||
| units: amu*angstrom^2 | ||
| value: | ||
| class: np_array | ||
| object: | ||
| - 2.554199931314157 | ||
| - 14.401630827087603 | ||
| - 16.955829291310987 | ||
| quantum: false | ||
| rotationalConstant: | ||
| class: ArrayQuantity | ||
| units: cm^-1 | ||
| value: | ||
| class: np_array | ||
| object: | ||
| - 6.599964570774655 | ||
| - 1.170536118842977 | ||
| - 0.9942084674081487 | ||
| symmetry: 1 | ||
| - class: HarmonicOscillator | ||
| frequencies: | ||
| class: ArrayQuantity | ||
| units: cm^-1 | ||
| value: | ||
| class: np_array | ||
| object: | ||
| - 1070.8598719116762 | ||
| - 1102.8428501327883 | ||
| - 1156.461372444652 | ||
| - 1360.2447152150203 | ||
| - 1482.2991207234968 | ||
| - 1715.3876054105042 | ||
| - 3000.8520252613916 | ||
| - 3102.7539960169784 | ||
| - 3449.588727421662 | ||
| quantum: true | ||
| number: | ||
| class: ArrayQuantity | ||
| value: | ||
| class: np_array | ||
| object: | ||
| - 6.0 | ||
| - 1.0 | ||
| - 1.0 | ||
| - 7.0 | ||
| - 1.0 | ||
| optical_isomers: 1 | ||
| spin_multiplicity: 1 | ||
| datetime: 2020-01-15 20:31 | ||
| energy_transfer_model: | ||
| T0: | ||
| class: ScalarQuantity | ||
| units: K | ||
| value: 300.0 | ||
| alpha0: | ||
| class: ScalarQuantity | ||
| units: kJ/mol | ||
| value: 3.5886 | ||
| class: SingleExponentialDown | ||
| n: 0.85 | ||
| frequency_scale_factor: 0.98789376345 | ||
| inchi: InChI=1S/CH3N/c1-2/h2H,1H2 | ||
| inchi_key: WDWDWGRYHDPSDS-UHFFFAOYSA-N | ||
| is_ts: false | ||
| label: CH2NH_GS | ||
| level_of_theory: ccsd(t)-f12/cc-pvqz-f12 | ||
| molecular_weight: | ||
| class: ScalarQuantity | ||
| units: amu | ||
| value: 29.041263028275246 | ||
| smiles: C=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: 90.04461855374207 | ||
| 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: 929.0351531097366 | ||
| Tmin: | ||
| class: ScalarQuantity | ||
| units: K | ||
| value: 10.0 | ||
| class: NASAPolynomial | ||
| coeffs: | ||
| class: np_array | ||
| object: | ||
| - 4.08222114580128 | ||
| - -0.004850902028028875 | ||
| - 3.0666770341789037e-05 | ||
| - -3.082088922692662e-08 | ||
| - 1.0083899185706911e-11 | ||
| - 10827.213177161942 | ||
| - 4.372647805595436 | ||
| polynomial2: | ||
| Tmax: | ||
| class: ScalarQuantity | ||
| units: K | ||
| value: 3000.0 | ||
| Tmin: | ||
| class: ScalarQuantity | ||
| units: K | ||
| value: 929.0351531097366 | ||
| class: NASAPolynomial | ||
| coeffs: | ||
| class: np_array | ||
| object: | ||
| - 0.8901428128919961 | ||
| - 0.013679059070920806 | ||
| - -6.97921272081837e-06 | ||
| - 1.7389788226959047e-09 | ||
| - -1.7011046269287458e-13 | ||
| - 11213.768047541436 | ||
| - 18.42594784828629 | ||
| thermo_data: | ||
| Cpdata: | ||
| class: ArrayQuantity | ||
| units: cal/(mol*K) | ||
| value: | ||
| class: np_array | ||
| object: | ||
| - 9.213634140721515 | ||
| - 10.60006649534414 | ||
| - 12.124136169535827 | ||
| - 13.634777266856286 | ||
| - 16.251975625324235 | ||
| - 18.200541211030536 | ||
| - 21.28968269749158 | ||
| - 22.895546542874406 | ||
| - 23.67837160715819 | ||
| H298: | ||
| class: ScalarQuantity | ||
| units: kcal/mol | ||
| value: 23.931566213291152 | ||
| S298: | ||
| class: ScalarQuantity | ||
| units: cal/(mol*K) | ||
| value: 54.23790822743784 | ||
| 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 | ||
| use_bond_corrections: true | ||
| use_hindered_rotors: false | ||
| xyz: |- | ||
| 5 | ||
| CH2NH_GS | ||
| C 0.58486800 0.02884100 -0.00001300 | ||
| H 1.07168000 1.01086200 -0.00001200 | ||
| H 1.24375400 -0.84087800 -0.00001800 | ||
| N -0.66593400 -0.15433500 -0.00001000 | ||
| H -1.16338800 0.73718400 -0.00000600 |
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