diff --git a/documentation/source/users/arkane/credits.rst b/documentation/source/users/arkane/credits.rst index 4e9d9cc9812..b5b01313960 100644 --- a/documentation/source/users/arkane/credits.rst +++ b/documentation/source/users/arkane/credits.rst @@ -9,7 +9,7 @@ Project Supervisors: - Prof. William H. Green (whgreen@mit.edu) - Prof. Richard H. West (r.west@northeastern.edu) - Prof. C. Franklin Goldsmith (franklin_Goldsmith@brown.edu) -- Asst. Prof. Alon Grinberg Dana (alon@technion.ac.il) +- Prof. Alon Grinberg Dana (alon@technion.ac.il) Developers: (rmg_dev@mit.edu) @@ -24,10 +24,10 @@ Developers: (rmg_dev@mit.edu) - Dr. D.S. Ranasinghe - Dr. R.J. Gillis - Dr. A.M. Payne -- Asst. Prof. Y.-P. Li -- X. Dong -- K.A. Spiekermann -- H. Wu +- Prof. Y.-P. Li +- Dr. X. Dong +- Dr. K.A. Spiekermann +- Mr. H. Wu - Dr. E.E. Dames - Dr. Z.J. Buras, - Dr. N.M. Vandewiele @@ -41,11 +41,4 @@ Developers: (rmg_dev@mit.edu) How to Cite *********** -A. Grinberg Dana, M.S. Johnson, J.W. Allen, S. Sharma, S. Raman, M. Liu, C.W. Gao, C.A. Grambow, M.J. Goldman, -D.S. Ranasinghe, R.J. Gillis, A.M. Payne, Y.-P. Li, X. Dong, K.A. Spiekermann, H. Wu, E.E. Dames, Z.J. Buras, -N.M. Vandewiele, N.W. Yee, S.S. Merchant, B. Buesser, C.A. Class, C.F. Goldsmith, R.H. West, W.H. Green, -"Automated reaction kinetics and network exploration (Arkane): -A statistical mechanics, thermodynamics, transition state theory, and master equation software", -*International Journal of Chemical Kinetics* 2023, 55(6), 300-323. - -DOI: `10.1002/kin.21637 `_ +Please refer to the ``Arkane`` reference in the `CITATIONS.bib file `_. \ No newline at end of file diff --git a/documentation/source/users/rmg/credits.rst b/documentation/source/users/rmg/credits.rst index faa4284055d..3ec2cd4ccc9 100755 --- a/documentation/source/users/rmg/credits.rst +++ b/documentation/source/users/rmg/credits.rst @@ -16,26 +16,29 @@ Project Supervisors: Current Developers: (rmg_dev@mit.edu) -- Dr. Alon Grinberg Dana +- Prof. Alon Grinberg Dana - Dr. Matt Johnson -- Yen-Ting Wang -- Xiaorui Dong -- Hao-Wei Pang +- Dr. Anna Doner - Oscar Wu -- Kevin Spiekermann - Jonathan Zheng - Jackson Burns - Nathan Morgan +- Prof. Richard H. West - Prof. C. Franklin Goldsmith -- Dr. Katrin Blondal - Dr. Bjarne Kreitz +- Chao Xu - Chris Blais - Sevy Harris - Nora Khalil Previous Developers: +- Dr. Xiaorui Dong +- Dr. Hao-Wei Pang +- Dr. Kevin Spiekermann +- Yen-Ting Wang - Dr. Joshua W. Allen +- Dr. Katrin Blondal - Dr. Yunsie Chung - Dr. David Farina - Dr. Mark Goldman @@ -66,25 +69,4 @@ Previous Developers: How to Cite *********** -C.W. Gao, J.W. Allen, W.H. Green, R.H. West, -"Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms", -*Computer Physics Communications* 2016, 203, 212-225. - -DOI: `10.1016/j.cpc.2016.02.013 `_ - - -M. Liu, A. Grinberg Dana, M.S. Johnson, M.J. Goldman, A. Jocher, A.M. Payne, C.A. Grambow, K. Han, N.W. Yee, -E.J. Mazeau, K. Blondal, R.H. West, C.F. Goldsmith, W.H. Green, -"Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation", -*Journal of Chemical Information and Modeling* 2021, 61(6), 2686–2696. - -DOI: `10.1021/acs.jcim.0c01480 `_ - - - -M.S. Johnson, X. Dong, A. Grinberg Dana, Y. Chung, D. Farina, R.J. Gillis, M. Liu, N.W. Yee, K. Blondal, -E. Mazeau, C.A. Grambow, A.M. Payne, K.A. Spiekermann, H.-W. Pang, C.F. Goldsmith, R.H. West, W.H. Green, -"The RMG Database for Chemical Property Prediction", -*Chemical Information* 2022, 62(20), 4906–4915. - -DOI: `10.1021/acs.jcim.2c00965 `_ +Please refer to the ``RMG``, ``RMG3``, and ``RMG_Database`` citations in the `CITATIONS.bib file `_. \ No newline at end of file diff --git a/documentation/source/users/rmg/database/kinetics.rst b/documentation/source/users/rmg/database/kinetics.rst index 7c1a1a61952..3ec2953d5fa 100644 --- a/documentation/source/users/rmg/database/kinetics.rst +++ b/documentation/source/users/rmg/database/kinetics.rst @@ -52,150 +52,7 @@ Kinetic libraries should also be used in the cases where: * No family exists for the class of reaction * You are not confident about the accuracy of kinetic parameters -Below is a list of pre-packaged kinetics library reactions in RMG: - - -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Library |Description | -+=============================================================+==========================================================================================+ -|1989_Stewart_2CH3_to_C2H5_H |Chemically Activated Methyl Recombination to Ethyl (2CH3 -> C2H5 + H) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|2001_Tokmakov_H_Toluene_to_CH3_Benzene |H + Toluene = CH3 + Benzene | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|2005_Senosiain_OH_C2H2 |pathways on the OH + acetylene surface | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|2006_Joshi_OH_CO |pathways on OH + CO = HOCO = H + CO2 surface | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|2009_Sharma_C5H5_CH3_highP |Cyclopentadienyl + CH3 in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|2015_Buras_C2H3_C4H6_highP |Vinyl + 1,3-Butadiene and other C6H9 reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|biCPD_H_shift |Sigmatropic 1,5-H shifts on biCPD PES | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|BurkeH2O2inArHe |Comprehensive H2/O2 kinetic model in Ar or He atmosphere | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|BurkeH2O2inN2 |Comprehensive H2/O2 kinetic model in N2 atmosphere | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|C2H4+O_Klipp2017 |C2H4 + O intersystem crossing reactions, probably important for all C/H/O combustion | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|C10H11 |Cyclopentadiene pyrolysis in the presence of ethene | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|C3 |Cyclopentadiene pyrolysis in the presence of ethene | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|C6H5_C4H4_Mebel |Formation Mechanism of Naphthalene and Indene | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Chernov |Soot Formation with C1 and C2 Fuels (aromatic reactions only) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|CurranPentane |Ignition of pentane isomers | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Dooley |Methyl formate (contains several mechanisms) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|ERC-FoundationFuelv0.9 |Small molecule combustio (natural gas) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Ethylamine |Ethylamine pyrolysis and oxidation | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|FFCM1(-) |Foundational Fuel Chemistry Model Version 1.0 (excited species removed) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2005_Ismail_C6H5_C4H6_highP |Phenyl + 1,3-Butadiene and other C10H11 reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2012_Matsugi_C3H3_C7H7_highP |Propargyl + Benzyl and other C10H10 reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2016_Mebel_C9H9_highP |C9H9 reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2016_Mebel_C10H9_highP |C10H9 reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2016_Mebel_Indene_CH3_highP |CH3 + Indene in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2017_Buras_C6H5_C3H6_highP |Phenyl + Propene and other C9H11 reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2017_Mebel_C6H4C2H_C2H2_highP |C10H7 HACA reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C2H2_highP |C8H7 HACA reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C4H4_highP |Phenyl + Vinylacetylene and other C10H9 reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/2017_Mebel_C6H5C2H2_C2H2_highP |C10H9 HACA reactions in high-P limit | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|First_to_Second_Aromatic_Ring/phenyl_diacetylene_effective |Effective Phenyl + Diacetylene rates to Benzofulvenyl and 2-Napthyl | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Fulvene_H |Cyclopentadiene pyrolysis in the presence of ethene | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|GRI-HCO |The `HCO <=> H + CO` reaction | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|GRI-Mech3.0 |Gas Research Institute natural gas mechanism optimized for 1 atm (discontinued Feb. 2000) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|GRI-Mech3.0-N |GRI-Mech3.0 including nitrogen chemistry (NOx from N2) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Glarborg |Mechanisms by P. Glarborg, assorted by carbon number | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|JetSurF2.0 |Jet Surrogate Fuel model up tp C12 (excited species removed) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Klippenstein_Glarborg2016 |Methane oxidation at high pressures and intermediate temperatures | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Lai_Hexylbenzene |Alkylaromatic reactions for hexylbenzene | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Mebel_C6H5_C2H2 |Pathways from benzene to naphthalene | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Mebel_Naphthyl |Reactions of naphthyl-1 and naphthyl-2 | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Methylformate |Methyl formate | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Narayanaswamy |Oxidation of substituted aromatic species (aromatic reactions only) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Nitrogen_Dean_and_Bozzelli |Combustion Chemistry of Nitrogen | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Nitrogen_Glarborg_Gimenez_et_al |High pressure C2H4 oxidation with nitrogen chemistry | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Nitrogen_Glarborg_Lucassen_et_al |Fuel-nitrogen conversion in the combustion of small amines | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Nitrogen_Glarborg_Zhang_et_al |Premixed nitroethane flames at low pressure | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|NOx |important NOx related reactions, e.g., thermal & prompt NO, N2O | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|NOx/LowT |Low temperature kinetics (~<1000K) for selected reactions from the NOx library | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|OxygenSingTrip |Reactions of singlet and triplet oxygen | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|SOx |important SOx related reactions, e.g., H-S, C-S, SOx | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/DMDS |Dimethyl disulfide (CH3SSCH3) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/DMS |Dimethyl disulfide (CH3SSCH3) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/DTBS |Di-tert-butyl Sulfide (C4H9SSC4H9) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/GlarborgBozzelli |SO2 effect on moist CO oxidation with and without NO | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/GlarborgH2S |H2S oxidation at high pressures | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/GlarborgMarshall |OCS chemistry | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/GlarborgNS |Interactions between nitrogen and sulfur species in combustion | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/Hexanethial_nr |Hexyl sulfide (C6H13SC6H13) + hexadecane (C16H34) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/Sendt |Small sulfur molecule | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/TP_Song |Thiophene (C4H4S, aromatic) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|Sulfur/Thial_Hydrolysis |Thioformaldehyde (CH2S) and thioacetaldehyde (C2H4S) to COS and CO2 | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|TEOS |Organic oxidized silicone | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|c-C5H5_CH3_Sharma |Cyclopentadienyl + CH3 | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|combustion_core |Leeds University natural gas mechanism (contains versions 2-5) | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|fascella |Cyclopentadienyl + acetyl | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|kislovB |Formation of indene in combustion | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|naphthalene_H |Cyclopentadiene pyrolysis in the presence of ethene Part 1 | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|vinylCPD_H |Cyclopentadiene pyrolysis in the presence of ethene Part 2 | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ -|PrimaryH2O2 |Updated rate parameters for the H2O2 system that include ter-molecular reactions | -+-------------------------------------------------------------+------------------------------------------------------------------------------------------+ +`A full list of the libraries can be found on the RMG website `_ (please allow 1-2 minutes for the website to load). .. _kinetics_families_db: @@ -212,237 +69,7 @@ Each reaction family contains the files: * training.py containing a training set for the family * rules.py containing kinetic parameters for rules -There are currently 74 reaction families in RMG: - -.. |f00| image:: images/kinetics_families/1+2_Cycloaddition.png - :scale: 40% -.. |f01| image:: images/kinetics_families/1,2-Birad_to_alkene.png - :scale: 40% -.. |f02| image:: images/kinetics_families/1,2_Insertion_CO.png - :scale: 40% -.. |f03| image:: images/kinetics_families/1,2_Insertion_carbene.png - :scale: 40% -.. |f04| image:: images/kinetics_families/1,2_NH3_elimination.png - :scale: 40% -.. |f05| image:: images/kinetics_families/1,2_shiftC.png - :scale: 40% -.. |f06| image:: images/kinetics_families/1,2_shiftS.png - :scale: 40% -.. |f07| image:: images/kinetics_families/1,3_Insertion_CO2.png - :scale: 40% -.. |f08| image:: images/kinetics_families/1,3_Insertion_ROR.png - :scale: 40% -.. |f09| image:: images/kinetics_families/1,3_Insertion_RSR.png - :scale: 40% -.. |f10| image:: images/kinetics_families/1,3_NH3_elimination.png - :scale: 40% -.. |f75| image:: images/kinetics_families/1,3_sigmatropic_rearrangement.png - :scale: 40% -.. |f11| image:: images/kinetics_families/1,4_Cyclic_birad_scission.png - :scale: 40% -.. |f12| image:: images/kinetics_families/1,4_Linear_birad_scission.png - :scale: 40% -.. |f13| image:: images/kinetics_families/2+2_cycloaddition.png - :scale: 40% -.. |f17| image:: images/kinetics_families/6_membered_central_C-C_shift.png - :scale: 40% -.. |f18| image:: images/kinetics_families/Baeyer-Villiger_step1_cat.png - :scale: 40% -.. |f19| image:: images/kinetics_families/Baeyer-Villiger_step2.png - :scale: 40% -.. |f20| image:: images/kinetics_families/Baeyer-Villiger_step2_cat.png - :scale: 40% -.. |f21| image:: images/kinetics_families/Bimolec_Hydroperoxide_Decomposition.png - :scale: 40% -.. |f22| image:: images/kinetics_families/Birad_R_Recombination.png - :scale: 40% -.. |f23| image:: images/kinetics_families/Birad_recombination.png - :scale: 40% -.. |f24| image:: images/kinetics_families/CO_Disproportionation.png - :scale: 40% -.. |f25| image:: images/kinetics_families/Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH.png - :scale: 40% -.. |f26| image:: images/kinetics_families/Cyclic_Ether_Formation.png - :scale: 40% -.. |f27| image:: images/kinetics_families/Cyclic_Thioether_Formation.png - :scale: 40% -.. |f28| image:: images/kinetics_families/Cyclopentadiene_scission.png - :scale: 40% -.. |f29| image:: images/kinetics_families/Diels_alder_addition.png - :scale: 40% -.. |f30| image:: images/kinetics_families/Disproportionation.png - :scale: 40% -.. |f31| image:: images/kinetics_families/HO2_Elimination_from_PeroxyRadical.png - :scale: 40% -.. |f32| image:: images/kinetics_families/H_Abstraction.png - :scale: 40% -.. |f33| image:: images/kinetics_families/Intra_2+2_cycloaddition_Cd.png - :scale: 40% -.. |f34| image:: images/kinetics_families/Intra_5_membered_conjugated_C=C_C=C_addition.png - :scale: 40% -.. |f35| image:: images/kinetics_families/Intra_Diels_alder_monocyclic.png - :scale: 40% -.. |f36| image:: images/kinetics_families/Intra_Disproportionation.png - :scale: 40% -.. |f37| image:: images/kinetics_families/Intra_RH_Add_Endocyclic.png - :scale: 40% -.. |f38| image:: images/kinetics_families/Intra_RH_Add_Exocyclic.png - :scale: 40% -.. |f39| image:: images/kinetics_families/Intra_R_Add_Endocyclic.png - :scale: 40% -.. |f40| image:: images/kinetics_families/Intra_R_Add_ExoTetCyclic.png - :scale: 40% -.. |f41| image:: images/kinetics_families/Intra_R_Add_Exo_scission.png - :scale: 40% -.. |f42| image:: images/kinetics_families/Intra_R_Add_Exocyclic.png - :scale: 40% -.. |f43| image:: images/kinetics_families/Intra_Retro_Diels_alder_bicyclic.png - :scale: 40% -.. |f44| image:: images/kinetics_families/Intra_ene_reaction.png - :scale: 40% -.. |f45| image:: images/kinetics_families/Korcek_step1.png - :scale: 40% -.. |f46| image:: images/kinetics_families/Korcek_step1_cat.png - :scale: 40% -.. |f47| image:: images/kinetics_families/Korcek_step2.png - :scale: 40% -.. |f48| image:: images/kinetics_families/Peroxyl_Disproportionation.png - :scale: 40% -.. |f49| image:: images/kinetics_families/Peroxyl_Termination.png - :scale: 40% -.. |f50| image:: images/kinetics_families/R_Addition_COm.png - :scale: 40% -.. |f51| image:: images/kinetics_families/R_Addition_CSm.png - :scale: 40% -.. |f52| image:: images/kinetics_families/R_Addition_MultipleBond.png - :scale: 40% -.. |f53| image:: images/kinetics_families/R_Recombination.png - :scale: 40% -.. |f54| image:: images/kinetics_families/Singlet_Carbene_Intra_Disproportionation.png - :scale: 40% -.. |f55| image:: images/kinetics_families/Singlet_Val6_to_triplet.png - :scale: 40% -.. |f56| image:: images/kinetics_families/SubstitutionS.png - :scale: 40% -.. |f57| image:: images/kinetics_families/Substitution_O.png - :scale: 40% -.. |f58| image:: images/kinetics_families/Surface_Abstraction.png - :scale: 40% -.. |f59| image:: images/kinetics_families/Surface_Adsorption_Bidentate.png - :scale: 40% -.. |f60| image:: images/kinetics_families/Surface_Adsorption_Dissociative.png - :scale: 40% -.. |f61| image:: images/kinetics_families/Surface_Adsorption_Double.png - :scale: 40% -.. |f62| image:: images/kinetics_families/Surface_Adsorption_Single.png - :scale: 40% -.. |f63| image:: images/kinetics_families/Surface_Adsorption_vdW.png - :scale: 40% -.. |f64| image:: images/kinetics_families/Surface_Bidentate_Dissociation.png - :scale: 40% -.. |f65| image:: images/kinetics_families/Surface_Dissociation.png - :scale: 40% -.. |f66| image:: images/kinetics_families/Surface_Dissociation_vdW.png - :scale: 40% -.. |f67| image:: images/kinetics_families/Surface_Recombination.png - :scale: 40% -.. |f68| image:: images/kinetics_families/intra_H_migration.png - :scale: 40% -.. |f69| image:: images/kinetics_families/intra_NO2_ONO_conversion.png - :scale: 40% -.. |f70| image:: images/kinetics_families/intra_OH_migration.png - :scale: 40% -.. |f71| image:: images/kinetics_families/intra_substitutionCS_cyclization.png - :scale: 40% -.. |f72| image:: images/kinetics_families/intra_substitutionCS_isomerization.png - :scale: 40% -.. |f73| image:: images/kinetics_families/intra_substitutionS_cyclization.png - :scale: 40% -.. |f74| image:: images/kinetics_families/intra_substitutionS_isomerization.png - :scale: 40% -.. |f76| image:: images/kinetics_families/lone_electron_pair_bond.png - :scale: 40% - -.. table:: - :widths: 40 60 - - ===================================================== ===== - **1+2_Cycloaddition** |f00| - **1,2-Birad_to_alkene** |f01| - **1,2_Insertion_CO** |f02| - **1,2_Insertion_carbene** |f03| - **1,2_NH3_elimination** |f04| - **1,2_shiftC** |f05| - **1,2_shiftS** |f06| - **1,3_Insertion_CO2** |f07| - **1,3_Insertion_ROR** |f08| - **1,3_Insertion_RSR** |f09| - **1,3_NH3_elimination** |f10| - **1,3_sigmatropic_rearrangement** |f75| - **1,4_Cyclic_birad_scission** |f11| - **1,4_Linear_birad_scission** |f12| - **2+2_cycloaddition** |f13| - **6_membered_central_C-C_shift** |f17| - **Baeyer-Villiger_step1_cat** |f18| - **Baeyer-Villiger_step2** |f19| - **Baeyer-Villiger_step2_cat** |f20| - **Bimolec_Hydroperoxide_Decomposition** |f21| - **Birad_R_Recombination** |f22| - **Birad_recombination** |f23| - **CO_Disproportionation** |f24| - **Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH** |f25| - **Cyclic_Ether_Formation** |f26| - **Cyclic_Thioether_Formation** |f27| - **Cyclopentadiene_scission** |f28| - **Diels_alder_addition** |f29| - **Disproportionation** |f30| - **HO2_Elimination_from_PeroxyRadical** |f31| - **H_Abstraction** |f32| - **Intra_2+2_cycloaddition_Cd** |f33| - **Intra_5_membered_conjugated_C=C_C=C_addition** |f34| - **Intra_Diels_alder_monocyclic** |f35| - **Intra_Disproportionation** |f36| - **Intra_RH_Add_Endocyclic** |f37| - **Intra_RH_Add_Exocyclic** |f38| - **Intra_R_Add_Endocyclic** |f39| - **Intra_R_Add_ExoTetCyclic** |f40| - **Intra_R_Add_Exo_scission** |f41| - **Intra_R_Add_Exocyclic** |f42| - **Intra_Retro_Diels_alder_bicyclic** |f43| - **Intra_ene_reaction** |f44| - **Korcek_step1** |f45| - **Korcek_step1_cat** |f46| - **Korcek_step2** |f47| - **Peroxyl_Disproportionation** |f48| - **Peroxyl_Termination** |f49| - **R_Addition_COm** |f50| - **R_Addition_CSm** |f51| - **R_Addition_MultipleBond** |f52| - **R_Recombination** |f53| - **Singlet_Carbene_Intra_Disproportionation** |f54| - **Singlet_Val6_to_triplet** |f55| - **SubstitutionS** |f56| - **Substitution_O** |f57| - **Surface_Abstraction** |f58| - **Surface_Adsorption_Bidentate** |f59| - **Surface_Adsorption_Dissociative** |f60| - **Surface_Adsorption_Double** |f61| - **Surface_Adsorption_Single** |f62| - **Surface_Adsorption_vdW** |f63| - **Surface_Bidentate_Dissociation** |f64| - **Surface_Dissociation** |f65| - **Surface_Dissociation_vdW** |f66| - **Surface_Recombination** |f67| - **intra_H_migration** |f68| - **intra_NO2_ONO_conversion** |f69| - **intra_OH_migration** |f70| - **intra_substitutionCS_cyclization** |f71| - **intra_substitutionCS_isomerization** |f72| - **intra_substitutionS_cyclization** |f73| - **intra_substitutionS_isomerization** |f74| - **lone_electron_pair_bond** |f76| - ===================================================== ===== - +`A full list of the kinetic families can be found on the RMG website `_ (please allow 1-2 minutes for the website to load). Recipe ------ diff --git a/documentation/source/users/rmg/faq.rst b/documentation/source/users/rmg/faq.rst index 2d2b3acc1e2..aa950a8d70b 100644 --- a/documentation/source/users/rmg/faq.rst +++ b/documentation/source/users/rmg/faq.rst @@ -9,52 +9,19 @@ We have compiled some common questions about installing and using RMG below. For any other questions related to RMG and its usage and installation, please post an issue on our `GitHub issues page `_, where you can also search for any previous reports of your issue. -Alternatively, you can also ask questions via the `RMG-Py chat room `_ -or by contacting us directly at rmg_dev@mit.edu. +Alternatively, you can contact us directly at rmg_dev@mit.edu. Installing RMG ============== -#. **How can I install RMG-Py without Anaconda?** - - Usually we don't recommend installing RMG-Py without Anaconda because it takes longer and is easier to get trouble - with package management. But one still can try direct installation on Linux or MacOS by following - :ref:`Linux instruction` or :ref:`MacOS instruction`. The RMG team does not use this install approach - internally any more, so these instructions are not actively maintained. - -#. **Why does RMG-Py not work natively on Windows?** +#. **Why does RMG-Py not work natively from source on Windows?** One major challenge with supporting Windows is ensuring that all of our dependencies support Windows. This becomes non-trivial as we add more dependencies to support increasing RMG functionality. Ensuring that code within RMG is platform-agnostic is also challenging, since it is rarely the first priority for new development because our main focus is on research. -#. **What is the recommended way to run RMG-Py on Windows?** - - The currently recommended way to run RMG on Windows is to set up a Linux environment. There are multiple ways you - can approach this. Windows 10 supports a Linux subsystem which allows one to set up a Linux environment within - Windows without using virtualization. You can find instructions on setting up RMG within the Linux subsystem - :ref:`here`. - - Another option would be to set up a full Linux virtual machine using something like VirtualBox or VMWare Workstation. - The benefit of this option is being able to run in a full Linux environment. However, running two operating systems - simultaneously does result in excess resource overhead, so it may not be suitable for running extended RMG jobs. - Instructions for setting up a virtual machine can be found :ref:`here`. - - A third option that we are currently beginning to explore using `Docker `_, which is a - container-based infrastructure which shares the same benefits as a virtual machine but with less overhead. There - are some test images of RMG-Py which can be found on `Docker Hub `_ if you would like to - give this a try. More detailed instructions will be made available once we officially support this approach. - -#. **Windows binary installation gives ``WindowsError: [Error 5]``?** - - Error 5 is access is denied, so this is either a permissions error, or an issue with the Windows file lock. - `These posts `_ suggest rebooting the computer (in case it's a file lock), - and running the anaconda prompt, from which you run ``conda create -c rmg --name rmg_env rmg rmgdatabase``, - as an administrator (in case it's a permissions error). Please checkout one example from a user having - `Windows binary installation issue `_. - Running RMG =========== @@ -98,24 +65,6 @@ Running RMG factors, such as poor thermochemistry or rate constants. Unfortunately, there is currently no good way to debug and fix these types of errors. -#. **Why did I get** ``Segmentation fault:11`` **after installing RMG on my machine?** - - **Segmentation fault** is a typical error in C code, caused by a program trying to read or write an illegal memory - location, i.e. one it is not allowed to access. The most common cause in RMG is a conflict between two different - versions of a shared library. RMG has some dependencies which are written in C++, e.g. rdkit, openbabel. If you - compile one of these with a different version of some compiler library, or you compile RMG using one version and - run it with another, you will often get a Segmentation fault. Chances are those packages are not up to date, or - maybe your environmental variable ``PATH`` is messed up so that the wrong version of something is being found. - Please see one example from a user having same - `Segmentation fault issue `_. - -#. **Why did I get** ``IOError: [Errno 13] Permission denied: 'C:\\RMG.log'`` - - You do not have permission to write to the log file. Try running the RMG from a different folder that you do have - write permission to, such as within your user's documents directory, or else try running the command prompt as an - Administrator (so that you have write permission everywhere). See for example - `issue #817 `_. - Miscellaneous ============= diff --git a/documentation/source/users/rmg/installation/dependencies.rst b/documentation/source/users/rmg/installation/dependencies.rst index ba8a3ad66c7..6cfbf0dc492 100644 --- a/documentation/source/users/rmg/installation/dependencies.rst +++ b/documentation/source/users/rmg/installation/dependencies.rst @@ -8,49 +8,9 @@ Dependencies List of Dependencies ==================== -Briefly, RMG depends on the following packages, almost all of which can be found in the `RMG anaconda channel `_ as binary packages. +A list of RMG's dependencies can be found in the ``environment.yml`` file on the `RMG GitHub page `_. -* **boost:** portable C++ source libraries -* **cairo:** a 2D vector graphics library with support for multiple backends including image buffers, PNG, PostScript, PDF, and SVG file output. Used for molecular diagram generation -* **cairocffi:** a set of Python bindings and object-oriented API for cairo -* **coverage:** code coverage measurement for Python -* **cython:** compiling Python modules to C for speed up -* **dde:** Data Driven Estimator for neural network thermochemistry prediction -* **ffmpeg:** (optional) used to encode videos, necessary for generating video flux diagrams -* **gaussian:** (optional) commerical software program for quantum mechanical calculations. Must be installed separately. -* **gcc:** GNU compiler collection for C,C++, and Fortran. (MinGW is used in windows) -* **gprof2dot:** converts Python profiling output to a dot graph -* **graphviz:** generating flux diagrams -* **jinja2:** Python templating language for html rendering -* **jupyter:** (optional) for using IPython notebooks -* **lpsolve:** mixed integer linear programming solver, used for resonance structure generation. Must also install Python extension. -* **markupsafe:** implements XML/HTML/XHTML markup safe strings for Python -* **matplotlib:** library for making plots -* **mock:** for unit-testing -* **mopac:** semi-empirical software package for QM calculations -* **mpmath:** for arbitrary-precision arithmetic used in Arkane -* **muq:** (optional) MIT Uncertainty Quantification library, used for global uncertainty analysis -* **networkx:** (optional) network analysis for reaction-path analysis IPython notebook -* **pytest:** advanced unit test controls -* **numpy:** fast matrix operations -* **openbabel:** chemical toolbox for speaking the many languages of chemical data -* **psutil:** system utilization diagnostic tool -* **pydas:** differential algebraic system solver -* **pydot:** interface to Dot graph language -* **pydqed:** constrained nonlinear optimization -* **pyparsing:** a general parsing module for python -* **pyrdl:** RingDecomposerLib for graph ring perception -* **pyyaml:** Python framework for YAML -* **pyzmq:** Python bindings for zeroMQ -* **quantities:** unit conversion -* **rdkit:** open-source cheminformatics toolkit -* **scipy:** fast mathematical toolkit -* **setuptools:** for packaging Python projects -* **sphinx:** documentation generation -* **symmetry:** calculating symmetry numbers of chemical point groups -* **xlwt:** generating Excel output files - .. _dependenciesRestrictions: License Restrictions on Dependencies @@ -60,7 +20,7 @@ All of RMG's dependencies except the ones listed below are freely available and * **pydas**: The DAE solvers used in the simulations come from `Linda Petzold's research group `_ at UCSB. For running sensitivity analysis in RMG, the DASPK 3.1 solver is required, which "is subject to copyright restrictions” for non-academic use. Please visit their website for more details. To run RMG without this restriction, one may switch to compiling with the DASSL solver instead in RMG, which is "available in the public domain.” -If you wish to do on-the-fly quantum chemistry calculations of thermochemistry (advisable for fused cyclic species in particular, where the ring corrections to group additive estimates are lacking), -the then you will need the third-party software for the QM calculations: +If you wish to do on-the-fly quantum chemistry calculations of thermochemistry (such as to improve estimates for fused cyclic species), +then you will need the third-party software for the QM calculations: -* **gaussian**: Gaussian03 and Gaussian09 are currently supported and commercially available. See `https://gaussian.com `_ for more details. +* **gaussian**: Gaussian16, Gaussian09 and Gaussian03 are currently supported and commercially available. See `https://gaussian.com `_ for more details. diff --git a/documentation/source/users/rmg/thermo.rst b/documentation/source/users/rmg/thermo.rst index b566ed48a45..53826b8c15d 100644 --- a/documentation/source/users/rmg/thermo.rst +++ b/documentation/source/users/rmg/thermo.rst @@ -154,7 +154,7 @@ On-the-fly Quantum-chemical calculation of Thermochemical Properties (QMTP) =========================================================================== An interface for performing on-the-fly quantum and force field calculations has been developed and integrated into RMG to complement the species thermochemistry databases and -group contribution methods [Magoon and Green]_. This interface is particularly interesting for the estimation of +group contribution methods [MagoonAndGreen]_. This interface is particularly interesting for the estimation of thermochemistry of molecules that are not present in one of the species thermochemistry databases, and which cannot be estimated with sufficient accuracy using the Benson group additivity framework. This pertains specifically to polycyclic fused ring containing species, whose ring strain cannot be modeled using @@ -283,7 +283,7 @@ References .. [Lay1995] Lay, T.; Bozzelli, J.; Dean, A.; Ritter, E. J. Phys. Chem. 1995, 99,14514-14527 -.. [Magoon and Green] Magoon, Gregory R., and William H. Green. "Design and implementation of a next-generation software interface for on-the-fly quantum and force field calculations in automated reaction mechanism generation." Computers & Chemical Engineering 52 (2013): 35-45. +.. [MagoonAndGreen] Magoon, Gregory R., and William H. Green. "Design and implementation of a next-generation software interface for on-the-fly quantum and force field calculations in automated reaction mechanism generation." Computers & Chemical Engineering 52 (2013): 35-45. .. [Allinger] Allinger, N. L., & Lii, J.-H. (2008). MM4(2008) and MM4(2003).