Simple Example

even a simple example is complicated to start, however building from this to more complicated examples becomes much easier as there is not much more growth in complexity.

Workflow

Following for a very simple example of the C2H6+H reaction system.

A simple theoretical treatment has been employed. Quantitative accuracy should not be expected.

1. electronic structure: low-level DFT methods, small basis-set MP2 energies

2. thermochemistry: RRHO

3. kinetics: RRHO with fixed transition state theory; energy transfer params estimated with internal scheme

The steps of the workflow as follows:

1. ESDriver: Generate geometries, frequencies, and energies PES specified in pes block (C2H6, C2H5, H, H2, TS)

2. ESDriver: Generate geometries, frequencies, and energies PES specified in spc block (CH4)

3. ThermoDriver: Build and run MESSPF for partition functions, then generate NASA polynomials for all species

4. kTPDriver: Build and run MESSRATEs for rate constants, then fit them

Input

To set up the chemical reactions and species for the input mechanism, we set

mechanism.dat file:

REACTIONS
    C2H6+H=C2H5+H2  1.0  0.0  0.0
END

species.csv file:

name,smiles,mult,charge
C2H6,'CC',1,0
C2H5,'C[CH2]',2,0
H,'[H]',2,0
H2,'[HH]',1,0
CH4,'CC',1,0

run.dat file:

input
    run_prefix = /fake/path/to/run
    save_prefix = /fake/path/to/save
end input

pes
    1: 1
end pes

spc
    5
end spc

els
    spc init_geom     runlvl=wbsgs   inplvl=wbsgs
    ts  find_ts       runlvl=wbsgs   inplvl=wbsgs
    all conf_energy   runlvl=mp2dz   inplvl=wbsgs
    all conf_hess     runlvl=wbsgs   inplvl=wbsgs
end els

thermo
    write_mess      kin_model=global  spc_model=global
    run_mess        kin_model=global  spc_model=global
    run_fits        kin_model=global  spc_model=global
end thermo

ktp
    write_mess      kin_model=global  spc_model=global
    run_mess
    run_fits        kin_model=global  spc_model=global
end ktp

Note that the pes specifies the global models. These models define the theoretical treatment used to build the MESS file and the rates

model.dat:

kin global
    pressures = (
        0.1  1.0  10.0 100.0
    )
    rate_temps = (
        500. 600. 700. 800. 900. 1000.
        1100. 1200. 1300. 1400. 1500
        1600. 1700. 1800. 1900. 2000.
    )
    therm_temps = (
        200. 300. 400. 500. 600. 700. 800. 900. 1000. 1100. 1200.
        1300. 1400. 1500. 1600. 1700. 1800. 1900. 2000. 2100. 2200.
        2300. 2400. 2500. 2600. 2700. 2800. 2900. 3000.
    )
    rate_fit = (
        fit_method = plog
        pdep_temps = [500.0, 1000.0]
        pdep_tol = 20.0
        pdep_pval = 1.0
        arrfit_dbltol = 15.0
    )
    therm_fit = (
        ref_scheme = basic
        ref_enes = ANL0
    )
end

spc global
    ene = (
        lvl1 = ccdz
    )
    rot = (
        mod = rigid
    )
    vib = (
        mod = harm
        geolvl = wbs
    )
    tors = (
        mod = 1dhr
        enelvl = wbs
        geolvl = wbs
    )
    symm = (
        mod = sampling
        geolvl = wbs
    )
    ts = (
        tunnel = eckart
        sadpt = fixed
        wells = fake
    )
end

theory.dat:

level wbsgs
    method = b3lyp
    basis = 6-31g*
    orb_res = RU
    program = psi4
end level

level mp2dz
    method = mp2
    basis = cc-pvdz
    orb_res = RR
    program = psi4
end level

Modify example for thermochem

Output

At the completion of ESDriver and kTPDriver, you will produce a MESS file and fit parameters.

MESS input file:

MESS input STR

Note that fake wells have been added

CHEMKIN output:

Rate params