Slight name change

README.md

@@ -2,7 +2,7 @@
   <a href="https://reactionmechanismgenerator.github.io/T3/"><img src="https://github.com/ReactionMechanismGenerator/T3/blob/main/grf/T3_logo_small.gif" alt="T3"></a>
 </p>
 
-# The Tandem Tool (T3) for automated kinetic model generation and refinement
+# The Tandem Tool (T3) for automated chemical kinetic model development
 
 ![Release](https://img.shields.io/badge/version-0.1.0-blue.svg)
 ![Build Status](https://github.com/ReactionMechanismGenerator/T3/actions/workflows/cont_int.yml/badge.svg)

docs/cite.md

@@ -2,15 +2,15 @@
 
 Text form:
 
-    A. Grinberg Dana, K.A. Spiekermann, W.H. Green, 
-    The Tandem Tool (T3) for automated kinetic model generation and refinement, 
+    C. Pieters, K. Kaplan, K.A. Spiekermann, W.H. Green, A. Grinberg Dana,
+    The Tandem Tool (T3) for automated chemical kinetic model development, 
     version 0.1.0, source code: https://github.com/ReactionMechanismGenerator/T3
 
 LaTeX form:
 
     @misc{T3,
-      author = {A. Grinberg Dana, K.A. Spiekermann, W.H. Green},
-      title = {The Tandem Tool (T3) for automated kinetic model generation and refinement. https://github.com/ReactionMechanismGenerator/T3, Version 0.1.0},
-      year = {2020},
+      author = {C. Pieters, K. Kaplan, K.A. Spiekermann, W.H. Green, A. Grinberg Dana,},
+      title = {The Tandem Tool (T3) for automated chemical kinetic model development. https://github.com/ReactionMechanismGenerator/T3, Version 0.1.0},
+      year = {2023},
       howpublished = {\url{https://github.com/ReactionMechanismGenerator/T3}},
     }

docs/index.md

@@ -3,7 +3,7 @@
   <img src="T3_logo_small.gif" alt="T3"></a>
 </p>
 <p align="center">
-    <em>The Tandem Tool for automated kinetic model generation and refinement</em>
+    <em>The Tandem Tool for automated chemical kinetic model development</em>
 </p>
 <p align="center">
 <a href="https://github.com/ReactionMechanismGenerator/T3/releases" target="_blank">

mkdocs.yml

@@ -1,6 +1,6 @@
 # Project information
 site_name: T3
-site_description: The Tandem Tool for automated kinetic model generation and refinement
+site_description: The Tandem Tool for automated chemical kinetic model development
 site_author: Alon Grinberg Dana
 site_url: https://reactionmechanismgenerator.github.io/T3/
 

t3/logger.py

@@ -123,7 +123,7 @@ def log_header(self):
                  f'################################################################\n'
                  f'#                                                              #\n'
                  f'#                  The   Tandem   Tool   (T3)                  #\n'
-                 f'#      Automated kinetic model generation and refinement       #\n'
+                 f'#       for automated chemical kinetic model development       #\n'
                  f'#                                                              #\n'
                  f'#                        Version: {VERSION}{" " * (10 - len(VERSION))}                   #\n'
                  f'#                                                              #\n'

tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c/t3.log

@@ -0,0 +1,74 @@
+T3 execution initiated on Tue Aug 15 16:39:28 2023
+
+################################################################
+#                                                              #
+#                  The   Tandem   Tool   (T3)                  #
+#       for automated chemical kinetic model development       #
+#                                                              #
+#                        Version: 0.1.0                        #
+#                                                              #
+################################################################
+
+
+The current git HEAD for T3 is:
+    a29e9884c7ce4b6c99ade2c31c9fba2202947440
+    Tue Aug 15 16:11:06 2023 +0300
+    (running on the c_conc_in_sim branch)
+
+Starting project xfa1014
+
+
+Using the following arguments:
+
+project: xfa1014
+project_directory: /home/alon/Code/T3/tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c
+verbose: info
+t3:
+  options:
+    all_core_species: True
+    max_T3_iterations: 5
+    max_RMG_exceptions_allowed: 5
+    library_name: FA
+  sensitivity:
+    adapter: RMGConstantTP
+    SA_threshold: 0.01
+    pdep_SA_threshold: 0.001
+    ME_methods: ['MSC']
+    top_SA_reactions: 0
+rmg:
+  database:
+    thermo_libraries: ['primaryThermoLibrary', 'BurkeH2O2', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo', 'Spiekermann_refining_elementary_reactions', 'CurranPentane', 'CBS_QB3_1dHR', 'primaryNS']
+    kinetics_libraries: ['primaryH2O2', 'NOx2018', '2006_Joshi_OH_CO', 'CurranPentane', 'Klippenstein_Glarborg2016', 'C2H4+O_Klipp2017', 'FFCM1(-)', 'C2H2_init', 'Narayanaswamy', 'Mebel_C6H5_C2H2', 'C10H11', 'C12H11_pdep', 'Lai_Hexylbenzene', '1989_Stewart_2CH3_to_C2H5_H', '2001_Tokmakov_H_Toluene_to_CH3_Benzene', '2003_Miller_Propargyl_Recomb_High_P', '2005_Senosiain_OH_C2H2', 'kislovB', 'c-C5H5_CH3_Sharma', 'fascella', '2006_Joshi_OH_CO', '2009_Sharma_C5H5_CH3_highP', '2015_Buras_C2H3_C4H6_highP', 'C3', 'Methylformate', 'C6H5_C4H4_Mebel', 'vinylCPD_H', 'Mebel_Naphthyl', 'Fulvene_H']
+  reactors: [{'type': 'gas batch constant T P', 'T': [500.0, 2000.0], 'P': [1.0, 100.0], 'termination_time': (60.0, 's')}]
+  species: [{'label': 'FA', 'concentration': (1.0, 4.0), 'smiles': 'OC=O', 'observable': True}, {'label': 'N2', 'concentration': 3.76, 'smiles': 'N#N', 'reactive': False}, {'label': 'O2', 'concentration': 1.0, 'smiles': '[O][O]'}, {'label': 'OH', 'smiles': '[OH]', 'observable': True}, {'label': 'HO2', 'smiles': 'O[O]', 'observable': True}, {'label': 'H', 'smiles': '[H]', 'observable': True}, {'label': 'H2', 'smiles': '[H][H]', 'observable': True}, {'label': 'CH3', 'smiles': '[CH3]', 'observable': True}, {'label': 'CO', 'smiles': '[C-]#[O+]', 'observable': True}, {'label': 'CO2', 'smiles': 'O=C=O', 'observable': True}, {'label': 'HOCO', 'smiles': 'O[C]=O', 'observable': True}, {'label': 'OCHO', 'smiles': '[O]C=O', 'observable': True}, {'label': 'CH2O', 'smiles': 'C=O', 'observable': True}, {'label': 'HCO', 'smiles': '[CH]=O', 'observable': True}]
+  model:
+    core_tolerance: [0.2, 0.1, 0.05, 0.01, 0.001]
+  pdep:
+    method: MSC
+    max_grain_size: 2.0
+    max_number_of_grains: 250
+    T: [300, 2500, 10]
+    P: [0.1, 110, 10]
+    interpolation: Chebyshev
+  options:
+    save_edge: False
+    save_html: True
+    save_simulation_profiles: True
+  species_constraints:
+    allowed: ['input species', 'seed mechanisms', 'reaction libraries']
+    max_C_atoms: 2
+    max_O_atoms: 4
+    max_N_atoms: 0
+    max_Si_atoms: 0
+    max_S_atoms: 0
+    max_heavy_atoms: 5
+    max_radical_electrons: 1
+    max_singlet_carbenes: 1
+    max_carbene_radicals: 0
+qm:
+  adapter: ARC
+  job_types:
+    rotors: False
+  level_of_theory: CBS-QB3
+
+Running a simulation using RMGConstantTP...