Add YAML support for thermodynamic and kinetics file

[jonlym]

Currently, pMuTT and OpenMKM relies on CTI files for thermodynamics and kinetics. Since Cantera supports YAML files, pMuTT and OpenMKM should be upgraded accordingly.

Additional context Refers to this issue: https://github.com/VlachosGroup/openmkm/issues/12 Cantera Documentation: https://cantera.org/documentation/dev/sphinx/html/yaml/index.html

[jonlym]

Cantera Objects to implement:

• [x] Units
• [x] Species
• [x] Reactions
• [x] Phases

OpenMKM Objects to implement:

• [x] BEPs
• [x] Lateral interactions

[jonlym]

The following script demonstrates pMuTT's ability to write Units and Species in Cantera's YAML format in commit 222c486

Units

pMuTT Python

import yaml
import numpy as np
from pmutt.empirical.nasa import Nasa, Nasa9, SingleNasa9
from pmutt.empirical.shomate import Shomate
from pmutt.cantera.units import Units

units = Units()
with open('test_yaml.yaml', 'w') as f_ptr:
    yaml.dump(units.to_yaml_dict(), f_ptr, default_flow_style=None)

Cantera YAML

{act_energy: cal/mol, energy: cal, length: cm, mass: kg, pressure: bar, quantity: molec,
  time: s}

Nasa7

pMuTT Python

H2O_nasa = Nasa(name='H2O',
                elements={'H': 2, 'O': 1},
                T_low=200., T_mid=1000., T_high=3500., n_sites=1,
                a_high=np.array([3.03399249E+00,
                                2.17691804E-03,
                                -1.64072518E-07,
                                -9.70419870E-11,
                                1.68200992E-14,
                                -3.00042971E+04,
                                4.96677010E+00]),
                a_low=np.array([4.19864056E+00,
                                -2.03643410E-03,
                                6.52040211E-06,
                                -5.48797062E-09,
                                1.77197817E-12,
                                -3.02937267E+04,
                                -8.49032208E-01]))
with open('test_yaml.yaml', 'a') as f_ptr:
    yaml.dump(H2O_nasa.to_yaml_dict(), f_ptr, default_flow_style=None)

Cantera YAML

composition: {H: 2, O: 1}
name: H2O
sites: 1
thermo:
  data:
  - [4.19864056, -0.0020364341, 6.52040211e-06, -5.48797062e-09, 1.77197817e-12, -30293.7267,
    -0.849032208]
  - [3.03399249, 0.00217691804, -1.64072518e-07, -9.7041987e-11, 1.68200992e-14, -30004.2971,
    4.9667701]
  model: NASA7
  temperature-ranges: [200.0, 1000.0, 3500.0]

Nasa9

pMuTT Python

A_nasa9 = Nasa9(name='ExampleNASA9',
                elements={'C': 1, 'H': 4},
                n_sites=1,
                nasas=[SingleNasa9(T_low=200., T_high=1000.,
                                   a=np.array([2.210371497E+04,
                                               -3.818461820E+02,
                                               6.082738360E+00,
                                               -8.530914410E-03,
                                               1.384646189E-05,
                                               -9.625793620E-09,
                                               2.519705809E-12,
                                               7.108460860E+02,
                                               -1.076003744E+01])),
                       SingleNasa9(T_low=1000., T_high=6000.,
                                   a=np.array([5.877124060E+05,
                                               -2.239249073E+03,
                                               6.066949220E+00,
                                               -6.139685500E-04,
                                               1.491806679E-07,
                                               -1.923105485E-11,
                                               1.061954386E-15,
                                               1.283210415E+04,
                                               -1.586640027E+01])),
                       SingleNasa9(T_low=6000., T_high=20000.,
                                   a=np.array([8.310139160E+08,
                                               -6.420733540E+05,
                                               2.020264635E+02,
                                               -3.065092046E-02,
                                               2.486903333E-06,
                                               -9.705954110E-11,
                                               1.437538881E-15,
                                               4.938707040E+06,
                                               -1.672099740E+03]))])

with open('test_yaml.yaml', 'a') as f_ptr:
    yaml.dump(A_nasa9.to_yaml_dict(), f_ptr, default_flow_style=None)

Cantera YAML

composition: {C: 1, H: 4}
name: ExampleNASA9
sites: 1
thermo:
  data:
  - [22103.71497, -381.846182, 6.08273836, -0.00853091441, 1.384646189e-05, -9.62579362e-09,
    2.519705809e-12, 710.846086, -10.76003744]
  - [587712.406, -2239.249073, 6.06694922, -0.00061396855, 1.491806679e-07, -1.923105485e-11,
    1.061954386e-15, 12832.10415, -15.86640027]
  - [831013916.0, -642073.354, 202.0264635, -0.03065092046, 2.486903333e-06, -9.70595411e-11,
    1.437538881e-15, 4938707.04, -1672.09974]
  model: NASA9
  reference-pressure: 1 bar
  temperature-ranges: [200.0, 1000.0, 6000.0, 20000.0]

Shomate

pMuTT Python

H2O_shomate = Shomate(name='H2O', 
                      elements={'H': 2, 'O': 1},
                      T_low=500., T_high=1700.,
                      a=np.array([30.09200,
                                  6.832514,
                                  6.793435,
                                  -2.534480,
                                  0.082139,
                                  -250.8810,
                                  223.3967,
                                  -241.8264]))
with open('test_yaml.yaml', 'a') as f_ptr:
    yaml.dump(H2O_shomate.to_yaml_dict(), f_ptr, default_flow_style=None)

Cantera YAML

composition: {H: 2, O: 1}
name: H2O
sites: null
thermo:
  data:
  - [30.092, 6.832514, 6.793435, -2.53448, 0.082139, -250.881, 223.3967, -241.8264]
  model: Shomate
  temperature-ranges: [500.0, 1700.0]

[jonlym]

OpenMKM Documentation updated with YAML syntax: https://vlachosgroup.github.io/openmkm/input

[jonlym]

Added support for Reactions, Phases, BEPs, and Lateral Interactions in commit 2ed1df77ec9a1e98d41d7d75b40eeae36f81a830.

May require further testing once new OpenMKM version is stable.