Added RMG thermo and kinetics scripts

to run RMG as standalone in its own env to get thermo and kinetics for comparisons

arc/scripts/__init__.py

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+import common

arc/scripts/common.py

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+"""
+This module contains functions which are shared across multiple ARC modules.
+As such, it should not import any other ARC module (specifically ones that use the logger defined here)
+to avoid circular imports.
+
+VERSION is the full ARC version, using `semantic versioning <https://semver.org/>`_.
+"""
+
+import argparse
+import os
+import yaml
+from typing import Union
+
+
+def parse_command_line_arguments(command_line_args=None):
+    """
+    Parse command-line arguments.
+
+    Args:
+        command_line_args: The command line arguments.
+
+    Returns:
+        The parsed command-line arguments by keywords.
+    """
+    parser = argparse.ArgumentParser(description='Automatic Rate Calculator (ARC)')
+    parser.add_argument('file', metavar='FILE', type=str, nargs=1, help='a file with input information')
+    args = parser.parse_args(command_line_args)
+    args.file = args.file[0]
+    return args
+
+
+def read_yaml_file(path: str) -> Union[dict, list]:
+    """
+    Read a YAML file (usually an input / restart file, but also conformers file)
+    and return the parameters as python variables.
+
+    Args:
+        path (str): The YAML file path to read.
+
+    Returns: Union[dict, list]
+        The content read from the file.
+    """
+    if not isinstance(path, str):
+        raise ValueError(f'path must be a string, got {path} which is a {type(path)}')
+    if not os.path.isfile(path):
+        raise ValueError(f'Could not find the YAML file {path}')
+    with open(path, 'r') as f:
+        content = yaml.load(stream=f, Loader=yaml.FullLoader)
+    return content
+
+
+def save_yaml_file(path: str, content: Union[list, dict]) -> None:
+    """
+    Save a YAML file (usually an input / restart file, but also conformers file).
+
+    Args:
+        path (str): The YAML file path to save.
+        content (list, dict): The content to save.
+    """
+    if not isinstance(path, str):
+        raise ValueError(f'path must be a string, got {path} which is a {type(path)}')
+    yaml_str = to_yaml(py_content=content)
+    if '/' in path and os.path.dirname(path) and not os.path.exists(os.path.dirname(path)):
+        os.makedirs(os.path.dirname(path))
+    with open(path, 'w') as f:
+        f.write(yaml_str)
+
+
+def to_yaml(py_content: Union[list, dict]) -> str:
+    """
+    Convert a Python list or dictionary to a YAML string format.
+
+    Args:
+        py_content (list, dict): The Python content to save.
+
+    Returns: str
+        The corresponding YAML representation.
+    """
+    yaml.add_representer(str, string_representer)
+    yaml_str = yaml.dump(data=py_content)
+    return yaml_str
+
+
+def string_representer(dumper, data):
+    """
+    Add a custom string representer to use block literals for multiline strings.
+    """
+    if len(data.splitlines()) > 1:
+        return dumper.represent_scalar(tag='tag:yaml.org,2002:str', value=data, style='|')
+    return dumper.represent_scalar(tag='tag:yaml.org,2002:str', value=data)

arc/scripts/libraries.yaml

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+thermo:
+  - primaryThermoLibrary
+  -  BurkeH2O2
+  -  Spiekermann_refining_elementary_reactions
+  -  thermo_DFT_CCSDTF12_BAC
+  -  DFT_QCI_thermo
+  -  CBS_QB3_1dHR
+  -  NH3
+  -  NitrogenCurran
+  -  CHON_G4
+  -  CN
+  -  NOx2018
+  -  FFCM1(-)
+  -  Butadiene_Dimerization
+  -  C10H11
+  -  s3_5_7_ane
+  -  Fulvene_H
+  -  naphthalene_H
+  -  vinylCPD_H
+  -  Lai_Hexylbenzene
+  -  Narayanaswamy
+  -  SABIC_aromatics_1dHR_extended
+  -  SABIC_aromatics_1dHR
+  -  SABIC_aromatics
+  -  heavy_oil_ccsdtf12_1dHR
+  -  bio_oil
+  -  Chernov
+  -  CurranPentane
+  -  Klippenstein_Glarborg2016
+kinetics:
+  - primaryH2O2
+  - primaryNitrogenLibrary
+  - Ethylamine
+  - primarySulfurLibrary
+  - Sulfur/DMDS
+  - Sulfur/DMS
+  - FFCM1(-)
+  - 2006_Joshi_OH_CO
+  - 2005_Senosiain_OH_C2H2
+  - NOx2018
+  - 2001_Tokmakov_H_Toluene_to_CH3_Benzene
+  - 2003_Miller_Propargyl_Recomb_High_P
+  - 2009_Sharma_C5H5_CH3_highP
+  - 2015_Buras_C2H3_C4H6_highP
+  - Butadiene_Dimerization
+  - C10H11
+  - C12H11_pdep
+  - C2H2_init
+  - C6H5_C4H4_Mebel
+  - Fulvene_H
+  - Mebel_Naphthyl
+  - Mebel_C6H5_C2H2
+  - biCPD_H_shift
+  - c-C5H5_CH3_Sharma
+  - fascella
+  - kislovB
+  - naphthalene_H
+  - vinylCPD_H