diff --git a/README.md b/README.md
index 7fb734cd..e147eebe 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
-# The Tandem Tool (T3) for automated kinetic model generation and refinement
+# The Tandem Tool (T3) for automated chemical kinetic model development
diff --git a/docs/cite.md b/docs/cite.md
index 997bc153..53fff743 100644
--- a/docs/cite.md
+++ b/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}},
}
diff --git a/docs/index.md b/docs/index.md
index 67378066..d57ec09f 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -3,7 +3,7 @@
- The Tandem Tool for automated kinetic model generation and refinement
+ The Tandem Tool for automated chemical kinetic model development
diff --git a/mkdocs.yml b/mkdocs.yml
index b7c1392e..e708f691 100644
--- a/mkdocs.yml
+++ b/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/
diff --git a/t3/logger.py b/t3/logger.py
index 97e8c294..c8c5df07 100644
--- a/t3/logger.py
+++ b/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'
diff --git a/tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c/t3.log b/tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c/t3.log
new file mode 100644
index 00000000..0b46f358
--- /dev/null
+++ b/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...