.. _fullchem-sim: ################### Fullchem simulation ################### ======== Overview ======== The GEOS-Chem :program:`fullchem` (aka "full-chemistry") simulation uses a detailed NOx-Ox-hydrocarbons-aerosols-halogens mechanism. You may choose one of several fullchem simulation options at :ref:`run directory creation time `. .. list-table:: :header-rows: 1 :align: left * - Option - Description * - :ref:`Standard ` - The default full chemistry simulation. Uses a simple SOA species and precursor. * - :ref:`Benchmark ` - The configuration used for performing GEOS-Chem benchmark simulations. Uses all of the species in the standard simulation, but also carries complex SOA species for diagnostic purposes. * - :ref:`Complex SOA ` - Replaces the simple SOA species and precursor with the `Pye et al. [2010] `_ complex SOA scheme. * - :ref:`Complex SOA plus semi-volatile POA ` - Replaces the simple SOA species and precursor with the Pye et al. 2010 complex SOA scheme, plus semi-volatile POA species. * - :ref:`Marine POA ` - Adds species MOPI (hydrophilic marine POA) and MOPO (hydrophobic marine POA). * - :ref:`Acid uptake on dust ` - Adds several species to track how acids are taken up by dust and other aerosols. * - :ref:`TOMAS ` - Replaces the default bulk aerosol scheme with TOMAS Aerosol Microphysics. * - :ref:`APM ` - Replaces the default bulk aerosol scheme with the APM Aerosol Microphysics. * - :ref:`RRTMG ` - Enables the RRTMG radiative transfer model, which can be used to compute radiative forcings for certain species. Most GEOS-Chem users typically run the :program:`Standard` simulation. .. _fullchem-sim-species: ========================== List of species, by option ========================== .. _fullchem-sim-standard: Standard -------- The :program:`Standard` fullchem option uses the following species: .. list-table:: Transported species (Standard option) :header-rows: 1 :align: left * - Species - Description - Formula - MW (g) * - ACET - Acetone - CH3C(O)CH3 - 58.09 * - ACTA - Acetic acid - CH3C(O)OH - 60.06 * - ACR - Acrolein - C3H4O - 56.06 * - AERI - Iodine on aerosol - I - 126.9 * - ALD2 - Acetaldehyde - CH3CHO - 44.06 * - ALK4 - Lumped C4+C5 Alkanes - not listed - 58.12 * - ALK4N2 - Lumped alkyl nitrate from ALK4 - RO2NO - 119.1 * - ALK4P - Peroxide from ALK4O2 - CH3CH2CH2CH2OOH - 90.14 * - ALK6 - Lumped >= C6 Alkanes - C7H16 - 100.2 * - AONITA - Aerosol-phase organonitrates from aromatics - C6H6O6N - 189.12 * - APAN - Peroxyacryloyl nitrate - C3H3NO5 - 133.06 * - APINP - Hydroperoxide from APIN - C10H18O3 - 186.28 * - APINN - 1st gen organic nitrate from APIN - C10H17NO4 - 215.28 * - AROMCHO - ACCOMECHO from MCM - C5H6O4 - 130.1 * - AROMP4 - Generic C4 product of aromatics - C4H4O2 - 68.08 * - AROMP5 - C5 unsaturated dicarbonyl - C5H6O2 - 98.1 * - AROMPN - Lumped PN from aromatics - C5H5NO8 - 207.1 * - ATOOH - ATO2 peroxide - CH3C(O)CH2OOH - 90.09 * - BALD - Benzaldehyde - C7H6O - 106.12 * - BCPI - Hydrophilic black carbon aerosol - C - 12.01 * - BCPO - Hydrophobic black carbon aerosol - C - 12.01 * - BENZ - Benzene - C6H6 - 78.12 * - BENZP - Phenyl hydroperoxide - C6H6O2 - 110.11 * - BPINO - Ketone from BPIN - C9H14O - 186.28 * - BPINN - Saturated 1st gen BPIN organic nitrate - C10H17NO4 - 215.28 * - BPINP - Peroxide from BPIN - C10H18O3 - 186.28 * - BPINOOH - 2nd-gen peroxide from BPIN - C9H14O3 - 186.28 * - BPINON - Saturated 2nd gen BPIN organic nitrate - C9H13NO4 - 215.28 * - Br - Atomic bromine - Br - 79.9 * - Br2 - Molecular Bromine - Br2 - 159.8 * - BrCl - Bromine chloride - BrCl - 115.45 * - BrNO2 - Nitryl bromide - BrNO2 - 125.91 * - BrNO3 - Bromine nitrate - BrNO3 - 141.91 * - BrO - Bromine monoxide - BrO - 95.9 * - BrSALA - Fine sea salt bromine - Br - 79.9 * - BrSALC - Coarse sea salt bromine - Br - 79.9 * - BUTDI - Butenedial - C4H4O2 - 84.07 * - BUTN - C4H6 alkyl nitrate - C4H7NO4 - 133.1 * - BZCO3H - Perbenzoic acid - C6H5CO3H - 138.12 * - BZPAN - Peroxybenzoylnitrate - C7H5O5N - 183.12 * - C96O2H - Peroxide from APIN 2nd gen - C9H16O3 - 186.28 * - C96N - Saturated 2nd gen monoterpene organic nitrate - C9H15NO4 - 215.28 * - C2H2 - Acetylene (aka Ethyne) - C2H2 - 26.05 * - C2H4 - Ethylene - C2H4 - 28.05 * - C2H6 - Ethane - C2H6 - 30.08 * - C3H8 - Propane - C3H8 - 44.11 * - C4H6 - 1,3-butadiene - C4H6 - 54.09 * - CCl4 - Carbon tetrachloride - CCl4 - 153.82 * - CFC11 - CFC-11 - CCl3F - 137.37 * - CFC113 - CFC-113 - C2Cl3F3 - 187.38 * - CFC114 - CFC-114 - C2Cl2F4 - 170.92 * - CFC115 - CFC-115 - C2ClF5 - 154.47 * - CFC12 - CFC-12 - CCl2F2 - 120.91 * - CH2Br2 - Dibromomethane - CH2Br2 - 173.83 * - CH2Cl2 - Dichloromethane - CH2Cl2 - 84.93 * - CH2I2 - Diiodomethane - CH2I2 - 267.84 * - CH2IBr - Bromoiodomethane - CH2IBr - 220.84 * - CH2ICl - Chloroiodomethane - CH2ICl - 176.38 * - CH2O - Formaldehyde - CH2O - 30.03 * - CH3Br - Methyl bromide - CH3Br - 94.94 * - CH3CCl3 - Methyl chloroform - CH3CCl3 - 133.35 * - CH3Cl - Chloromethane - CH3Cl - 50.45 * - CH3I - Methyl iodide - CH3I - 141.94 * - CH4 - not listed - CH4 - 16.04 * - CHBr3 - Bromoform - CHBr3 - 252.73 * - CHCl3 - Chloroform - CHCl3 - 119.35 * - Cl - Atomic chlorine - Cl - 35.45 * - Cl2 - Molecular chlorine - Cl2 - 70.9 * - Cl2O2 - Dichlorine dioxide - Cl2O2 - 102.91 * - ClNO2 - Nitryl chloride - ClNO2 - 81.45 * - ClNO3 - Chlorine nitrate - ClNO3 - 97.45 * - ClO - Chlorine monoxide - ClO - 51.45 * - ClOO - Chlorine dioxide - ClOO - 67.45 * - CLOCK - Clock tracer for diagnosing age of air - not listed - 1.0 * - CO - not listed - CO - 28.01 * - CSL - Cresols - C7H8O - 108.14 * - DMS - Dimethyl sulfide - (CH3)2S - 62.13 * - DSTbin1 - Dust aerosol, Reff = 0.151 :math:`\mu\text{m}` - not listed - 29.0 * - DSTbin2 - Dust aerosol, Reff = 0.253 :math:`\mu\text{m}` - not listed - 29.0 * - DSTbin3 - Dust aerosol, Reff = 0.402 :math:`\mu\text{m}` - not listed - 29.0 * - DSTbin4 - Dust aerosol, Reff = 0.818 :math:`\mu\text{m}` - not listed - 29.0 * - DSTbin5 - Dust aerosol, Reff = 1.491 :math:`\mu\text{m}` - not listed - 29.0 * - DSTbin6 - Dust aerosol, Reff = 2.417 :math:`\mu\text{m}` - not listed - 29.0 * - DSTbin7 - Dust aerosol, Reff = 3.721 :math:`\mu\text{m}` - not listed - 29.0 * - EBZ - Ethylbenzene - C8H10 - 106.167 * - EOH - Ethanol - C2H5OH - 46.07 * - ETHLN - Ethanol nitrate - CHOCH2ONO2 - 105.06 * - ETHN - hydroxy-nitrooxy-ethane - HOCH2CH2ONO2 - 107.07 * - ETHP - hydroxy-hydroperoxy-ethane - HOCH2CH2OOH - 78.07 * - ETNO3 - Ethyl nitrate - C2H5ONO2 - 91.08 * - ETP - Ethylhydroperoxide - CH3CH2OOH - 62.08 * - FURA - Furan - C4H4O - 68.07 * - GLYC - Glycoaldehyde - HOCH2CHO - 60.06 * - GLYX - Glyoxal - CHOCHO - 58.04 * - HACTA - Hydroxyacetic/glycolic acid - HOCH2CO2H - 76.0514 * - H1211 - Halon 1211, Freon 12B1 - CBrClF2 - 165.36 * - H1301 - Halon 1301, Freon 13B1 - CBrF3 - 148.91 * - H2402 - Halon 2402 - C2Br2F4 - 259.82 * - H2O - Water vapor - H2O - 18.02 * - H2O2 - Hydrogen peroxide - H2O2 - 34.02 * - HAC - Hydroxyacetone - HOCH2C(O)CH3 - 74.08 * - HBr - Hypobromic acid - HBr - 80.91 * - HC5A - isoprene-4,1-hydroxyaldehyde - C5H8O2 - 100.13 * - HCFC123 - HCFC-123, Freon 123 - C2HCl2F3 - 152.93 * - HCFC141b - HCFC-141b, Freon 141b - C(CH3)Cl2F - 116.94 * - HCFC142b - HCFC-142b, Freon 142b - C(CH3)ClF2 - 100.5 * - HCFC22 - HCFC-22, Freon 22 - CHClF2 - 86.47 * - HCl - Hydrochloric acid - HCl - 36.45 * - HCOOH - Formic acid - HCOOH - 46.03 * - HI - Hydrogen iodide - HI - 127.91 * - HMHP - Hydroxymethyl hydroperoxide - HOCH2OOH - 64.05 * - HMML - hydroxymethyl-methyl-a-lactone - C4H6O3 - 102.1 * - HMS - Hydroxymethanesulfonate - HOCH2SO3− - 111.1 * - HNO2 - Nitrous acid - HNO2 - 47.01 * - HNO3 - Nitric acid - HNO3 - 63.01 * - HNO4 - Peroxynitric acid - HNO4 - 79.01 * - HOBr - Hypobromous acid - HOBr - 96.91 * - HOCl - Hypochlorous acid - HOCl - 52.45 * - HOI - Hypoiodous acid - HOI - 143.89 * - HONIT - 2nd gen monoterpene organic nitrate - not listed - 215.0 * - HPALD1 - d-4,1-C5-hydroperoxyaldehyde - C5H8O3 - 116.13 * - HPALD2 - d-1,4-C5-hydroperoxyaldehyde - C5H8O3 - 116.13 * - HPALD3 - b-2,1-C5-hydroperoxyaldehyde - C5H8O3 - 116.13 * - HPALD4 - b-3,4-C5-hydroperoxyaldehyde - C5H8O3 - 116.13 * - HPETHNL - Hydroperoxy ethanal - HOOCH2CHO - 76.06 * - I - Atomic iodine - I - 126.9 * - I2 - Molecular iodine - I2 - 253.8 * - I2O2 - Diiodine dioxide - I2O2 - 285.8 * - I2O3 - Diiodine trioxide - I2O3 - 301.8 * - I2O4 - Diiodine tetraoxide - I2O4 - 317.8 * - IBr - Iodine monobromide - IBr - 206.9 * - ICHE - Isoprene hydroxy-carbonyl-epoxides - C5H8O3 - 116.13 * - ICl - Iodine monochloride - ICl - 162.45 * - ICN - Lumped isoprene carbonyl-nitrates - C5H7NO4 - 145.13 * - ICPDH - Isoprene dihydroxy hydroperoxycarbonyl - C5H10O5 - 150.15 * - IDC - Lumped isoprene dicarbonyls - C5H6O2 - 98.11 * - IDCHP - Isoprene dicarbonyl hydroxy dihydroperoxide - C5H8O5 - 148.13 * - IDHDP - Isoprene dihydroxy dihydroperoxide - C5H12O6 - 168.17 * - IDHPE - Isoprene dihydroxy hydroperoxy epoxide - C5H10O5 - 150.15 * - IDN - Lumped isoprene dinitrates - C5H8N2O6 - 192.15 * - IEPOXA - trans-Beta isoprene epoxydiol - C4H10O3 - 106.14 * - IEPOXB - cis-Beta isoprene epoxydiol - C4H10O3 - 106.14 * - IEPOXD - Delta isoprene epoxydiol - C4H10O3 - 106.14 * - IHN1 - Isoprene-d-4,1-hydroxynitrate - C5H9NO4 - 147.15 * - IHN2 - Isoprene-b-1,2-hydroxynitrate - C5H9NO4 - 147.15 * - IHN3 - Isoprene-b-4,3-hydroxynitrate - C5H9NO4 - 147.15 * - IHN4 - Isoprene-d-4,1-hydroxynitrate - C5H9NO4 - 147.15 * - INDIOL - Generic aerosol-phase organonitrate hydrolysis product - not listed - 102.0 * - INO - Nitrosyl iodide - INO - 156.91 * - INPB - Lumped b-hydroperoxy isoprene nitrates - C5H9NO5 - 163.15 * - INPD - Lumped d-hydroperoxy isoprene nitrates - C5H9NO5 - 163.15 * - IO - Iodine monoxide - IO - 142.9 * - IONITA - Aer-phase organic nitrate from isoprene precursors - not listed - 14.01 * - IONO - Nitryl iodide - IONO - 172.91 * - IONO2 - Iodine nitrate - IONO2 - 188.91 * - IPRNO3 - Isopropyl nitrate - C3H7ONO2 - 105.11 * - ISALA - Fine sea salt iodine - I - 126.9 * - ISALC - Coarse sea salt iodine - I - 126.9 * - ISOP - Isoprene - CH2=C(CH3)CH=CH2 - 68.13 * - ITCN - lumped isoprene tetrafunctional carbonylnitrates - C5H9NO7 - 195.15 * - ITHN - Lumped isoprene tetrafunctional hydroxynitrates - C5H11NO7 - 197.17 * - LIMAL - Aldehyde from limonene - C10H16O2 - 186.28 * - LIMKB - 2nd gen ketone from limonene - C10H16O3 - 186.28 * - LIMKET - Ketone from limonene - C10H16O2 - 186.28 * - LIMN - Saturated 1st gen limonene organic nitrate - C10H17NO4 - 215.28 * - LIMNB - Saturated 1st gen LIMO organic nitrate - C10H15NO4 - 215.28 * - LIMO - Limonene - C10H16 - 136.26 * - LIMO2H - Acid from LIMO - C10H18O3 - 186.28 * - LIMO3H - Peracid from LIMO - C10H18O4 - 186.28 * - LIMPAN - PAN from LIMO - C10H17NO4 - 215.28 * - LVOC - Gas-phase low-volatility non-IEPOX product of RIP ox - C5H14O5 - 154.19 * - LVOCOA - Aer-phase low-volatility non-IEPOX product of RIP ox - C5H14O5 - 154.19 * - MACR - Methacrolein - CH2=C(CH3)CHO - 70.1 * - MACR1OOH - Peracid from MACR - CH2=C(CH3)C(O)OOH - 102.1 * - MAP - Peroxyacetic acid - CH3C(O)OOH - 76.06 * - MCRDH - Dihydroxy-methacrolein - C4H8O3 - 104.12 * - MCRENOL - Lumped enols from MVK/MACR - C4H6O2 - 86.1 * - MCRHN - Nitrate from MACR - HOCH2C(ONO2)(CH3)CHO - 149.11 * - MCRHNB - Nitrate from MACR - O2NOCH2C(OH)(CH3)CHO - 149.11 * - MCRHP - Hydroxy-hydroperoxy-methacrolein - HOCH2C(OOH)(CH3)CHO - 120.12 * - MCT - Catechols and methyl catechols - C7H8O2 - 124.0 * - MEK - Methyl Ethyl Ketone - RC(O)R - 72.11 * - MEKPN - MEK peroxyacetyl nitrate - C3H5NO6 - 151.07 * - MENO3 - Methyl nitrate - CH3ONO2 - 77.05 * - MGLY - Methylglyoxal - CH3COCHO - 72.07 * - MOH - Methanol - CH3OH - 32.05 * - MONITA - Aer-phase organic nitrate from monoterpene precursors - not listed - 14.01 * - MONITS - Saturated 1st gen monoterpene organic nitrate - C10H17NO4 - 215.28 * - MONITU - Unsaturated 1st gen monoterpene organic nitrate - C10H17NO4 - 215.28 * - MP - Methyl hydro peroxide - CH3OOH - 48.05 * - MPAN - Peroxymethacroyl nitrate (PMN) - CH2=C(CH3)C(O)OONO2 - 147.1 * - MPN - Methyl peroxy nitrate - CH3O2NO2 - 93.05 * - MSA - Methyl sulfonic acid - CH4SO3 - 96.1 * - MTPA - a-pinene, b-pinene, sabinene, carene - not listed - 136.26 * - MTPO - Terpinene, terpinolene, myrcene, ocimene, other monoterpenes - not listed - 136.26 * - MVK - Methyl vinyl ketone - CH2=CHC(=O)CH3 - 70.09 * - MVKDH - dihydroxy-MVK - HOCH2CH2OHC(O)CH3 - 105.13 * - MVKHC - MVK hydroxy-carbonyl - C4H6O3 - 102.1 * - MVKHCB - MVK hydroxy-carbonyl - C4H6O3 - 102.1 * - MVKHP - MVK hydroxy-hydroperoxide - C4H8O4 - 120.12 * - MVKN - Nitrate from MVK - HOCH2CH(ONO2)C(=O)CH3 - 149.12 * - MVKPC - MVK hydroperoxy-carbonyl - OCHCH(OOH)C(O)CH3 - 118.1 * - MYRCO - Aldehyde or ketone from myrcene - C10H18O3 - 186.28 * - N2O - Nitrous oxide - N2O - 44.02 * - N2O5 - Dinitrogen pentoxide - N2O5 - 108.02 * - NH3 - Ammonia - NH3 - 17.04 * - NH4 - Ammonium - NH4 - 18.05 * - NIT - Inorganic nitrates - not listed - 62.01 * - NITs - Inorganic nitrates on surface of seasalt aerosol - not listed - 31.4 * - NO - Nitrogen oxide - NO - 30.01 * - NO2 - Nitrogen dioxide - NO2 - 46.01 * - NO3 - Nitrate radical - NO3 - 62.01 * - NPHEN - Nitrophenols - C6H5NO3 - 139.11 * - NPRNO3 - n-propyl nitrate - C3H7ONO2 - 105.11 * - O3 - Ozone - O3 - 48.0 * - OClO - Chlorine dioxide - OClO - 67.45 * - OCPI - Hydrophilic organic carbon aerosol - not listed - 12.01 * - OCPO - Hydrophobic organic carbon aerosol - not listed - 12.01 * - OCS - Carbonyl sulfide - COS - 60.07 * - OIO - Iodine dioxide - OIO - 158.9 * - PAN - Peroxyacetyl nitrate - CH3C(O)OONO2 - 121.06 * - pFe - Anthropogenic iron - Fe - 55.85 * - PHAN - Peroxyhydroxyacetic nitric anhydride - C2H3NO6 - 137.0483 * - PHEN - Phenol - C6H6O - 94.11 * - PIN - Saturated 1st gen monoterpene organic nitrate - C10H17NO4 - 215.28 * - PINAL - Pinonaldehyde - C10H16O2 - 186.28 * - PINONIC - Pinonic acid - C10H18O3 - 186.28 * - PINO3H - Pinonic peracid - C10H18O4 - 186.28 * - PINPAN - PAN from pinonaldehyde - C10H17NO4 - 215.28 * - PIP - Peroxide from MTPA - C10H18O3 - 186.28 * - PP - Peroxide from PO2 - HOCH2CH(OOH)CH3 - 92.11 * - PPN - Lumped peroxypropionyl nitrate - CH3CH2C(O)OONO2 - 135.08 * - PROPNN - Propanone nitrate - CH3C(=O)CH2ONO2 - 119.08 * - PRPE - Lumped >= C3 alkenes - C3H6 - 42.09 * - PRPN - Peroxide from PRN1 - O2NOCH2CH(OOH)CH3 - 137.11 * - PYAC - Pyruvic acid - C3H4O3 - 88.07 * - R4N2 - Lumped alkyl nitrate - RO2NO - 119.1 * - R4P - Peroxide from R4O2 - CH3CH2CH2CH2OOH - 90.14 * - R7N2 - C7 Lumped alkyl nitrate - RO2NO - 161.2 * - R7P - Peroxide from R7O2 - C7H16O2 - 132.2 * - RA3P - Peroxide from A3O2 - CH3CH2CH2OOH - 76.11 * - RB3P - Peroxide from B3O2 - CH3CH(OOH)CH3 - 76.11 * - RCHO - Lumped aldehyde >= C3 - CH3CH2CHO - 58.09 * - RCOOH - > C2 organic acids - C2H5C(O)OH - 74.09 * - RIPA - 1,2-ISOPOOH - C5H10O3 - 118.15 * - RIPB - 4,3-ISOPOOH - C5H10O3 - 118.15 * - RIPC - d-1,4-ISOPOOH - C5H10O3 - 118.15 * - RIPD - d-4,1-ISOPOOH - C5H10O3 - 118.15 * - RNO3 - Lumped aromatic nitrate - RO2NO - 203.15 * - RP - Peroxide from RCO3 - CH3CH2C(O)OOH - 90.09 * - SALA - Fine (0.01-0.05 :math:`\mu\text{m}`) sea salt aerosol - not listed - 31.4 * - SALAAL - Accumulation mode sea salt alkalinity - not listed - 31.4 * - SALACL - Chloride in Accumulation mode sea salt aerosol - not listed - 35.45 * - SALC - Coarse (0.5-8 :math:`\mu\text{m}`) sea salt aerosol - not listed - 31.4 * - SALCAL - Coarse mode sea salt alkalinity - not listed - 31.4 * - SALCCL - Chloride in Coarse mode sea salt aerosol - not listed - 35.45 * - SO2 - Sulfur dioxide - SO2 - 64.04 * - SO4 - Sulfate - SO4 - 96.06 * - SO4s - Sulfate on surface of seasalt aerosol - not listed - 31.4 * - SOAGX - Aerosol-phase glyoxal - C2H2O2 - 58.04 * - SOAIE - Aerosol-phase IEPOX - C5H10O3 - 118.15 * - SOAP - SOA Precursor - lumped species for simplified SOA parameterization - not listed - 150.0 * - SOAS - SOA Simple - simplified non-volatile SOA parameterization - not listed - 150.0 * - STYR - Styrene - C8H8 - 104.1491 * - TLFUONE - Aromatic furanones - C5H6O2 - 98.1 * - TMB - Trimethylbenzenes - C8H10 - 106.167 * - TOLU - Toluene - C7H8 - 92.15 * - XYLE - Xylene - C8H10 - 106.18 .. list-table:: Non-transported species (Standard option) :header-rows: 1 :align: left * - Species - Description - Formula - MW (g) * - A3O2 - Primary peroxy radical from C3H8 - CH3CH2CH2OO - 75.1 * - ACRO2 - Peroxy radical from ACR - C3H5O4 - 105.07 * - ACO3 - Peroxyacetyl radical for APAN - C3H3O3 - 87.054 * - ALK4N1 - Peroxy radical from ALK4N2 - C4H8NO5 - 150.13 * - ALK4O2 - Peroxy radical from ALK4 - C4H9O2 - 89.13 * - AROMRO2 - hydroxy-peroxy radical from aromatics - C6H7O3 - 127.0 * - AROMCO3 - Lumped aromatic peroxyacetyl radical - C5H5O6 - 161.09 * - ATO2 - Peroxy radical from acetone - CH3C(O)CH2O2 - 89.08 * - B3O2 - B3O2 - CH3CH(OO)CH3 - 75.1 * - BENZO - alkoxy radical from aromatics - C6H5O - 93.0 * - BENZO2 - peroxy radical from aromatics - C6H5O2 - 109.0 * - BRO2 - Peroxy radical from BENZ oxidation - C6H7O5 - 159.13 * - BUTO2 - peroxy radical from C4H6 - C4H7O3 - 103.097 * - BZCO3 - Acyl peroxy radical from benzaldehyde - C7H5O3 - 137.0 * - C4HVP1 - C4 hydroxy-vinyl peroxy radicals from HPALDS - C4H7O3 - 103.11 * - C4HVP2 - C4 hydroxy-vinyl peroxy radicals from HPALDS - C4H7O3 - 103.11 * - CH2OO - Criegee intermediate - CH2OO - 46.03 * - CH3CHOO - Criegee intermediate - CH3CHOO - 60.06 * - CO2 - Carbon dioxide - CO2 - 44.01 * - ETO - alkoxy radical from ETOO - HOCH2CH2O - 61.06 * - ETOO - peroxy radical from ethene - HOCH2CH2OO - 77.06 * - ETO2 - ETO2 - CH3CH2OO - 61.07 * - GCO3 - Peroxyacetyl radical for PHAN - HOCH2CO3 - 91.0428 * - H - Atomic hydrogen - H - 1.01 * - HO2 - Hydroperoxyl radical - HO2 - 33.01 * - HPALD1OO - HPALD1OO - C5H7O5 - 147.12 * - HPALD2OO - HPALD2OO - C5H7O5 - 147.12 * - ICHOO - Peroxy radical from IEPOXD - C5H9O5 - 149.14 * - ICNOO - Peroxy radicals from ICN - C5H8NO7 - 194.14 * - IDHNBOO - Peroxy radicals from INPB - C5H10NO7 - 196.16 * - IDHNDOO1 - Peroxy radicals from INPD - C5H10NO7 - 196.16 * - IDHNDOO2 - Peroxy radicals from INPD - C5H10NO7 - 196.16 * - IDNOO - IDNOO - C5H9N2O6 - 241.14 * - IEPOXAOO - Peroxy radical from trans-Beta isoprene epoxydiol - C5H8O5 - 149.14 * - IEPOXBOO - peroxy radical from cis-Beta isoprene epoxydiol - C5H9O5 - 149.14 * - IHOO1 - Peroxy radical from OH addition to isoprene at C1 - C5H9O3 - 117.14 * - IHOO4 - Peroxy radical from OH addition to isoprene at C4 - C5H9O3 - 117.14 * - IHPNBOO - Peroxy radicals from INPB - C5H10NO8 - 212.16 * - IHPNDOO - Peroxy radicals from INPD - C5H10NO8 - 212.16 * - IHPOO1 - Peroxy radical from ISOPOOH - C5H11O6 - 167.16 * - IHPOO2 - Peroxy radical from ISOPOOH - C5H11O6 - 167.16 * - IHPOO3 - Peroxy radical from ISOPOOH - C5H11O6 - 167.16 * - INA - Alkoxy radical from INO2D - C5H8NO4 - 146.14 * - INO2B - beta-peroxy radicals from isoprene + NO3 - C5H8NO5 - 162.14 * - INO2D - delta-peroxy radicals from isoprene + NO3 - C5H8NO5 - 162.14 * - ISOPNOO1 - Peroxy radicals from IHN2 - C5H10NO7 - 196.16 * - ISOPNOO2 - Peroxy radicals from IHN3 - C5H10NO7 - 196.16 * - KO2 - Peroxy radical from >3 ketones - C4H5O3 - 101.09 * - LBRO2H - Dummy species to track oxidation of BRO2 by HO2 - not listed - 159.13 * - LBRO2N - Dummy species to track oxidation of BRO2 by NO - not listed - 159.13 * - LIMO2 - Peroxy radical from LIMO - C10H17O3 - 185.27 * - APINO2 - Peroxy radical from APIN - C10H17O3 - 185.27 * - PINO3 - Acylperoxy radical from APIN - C10H17O3 - 185.27 * - C96O2 - 2nd-gen peroxy radical from APIN - C10H17O3 - 185.27 * - BPINO2 - Peroxy radical from BPIN - C10H17O3 - 185.27 * - BPINOO2 - 2nd-gen peroxy radical from BPIN - C10H17O3 - 185.27 * - LIMKO2 - 2nd-gen peroxy radical from LIMO - C10H17O3 - 185.27 * - LIMO3 - Acylperoxy radical from LIMO - C10H17O3 - 185.27 * - LISOPOH - Dummy species to track oxidation of ISOP by OH - not listed - 68.13 * - LISOPNO3 - Dummy species to track oxidation of ISOP by NO3 - not listed - 68.13 * - LNRO2H - Dummy species to track oxidation of NRO2 by HO2 - not listed - 159.17 * - LNRO2N - Dummy species to track oxidation of NRO2 by NO - not listed - 159.17 * - LTRO2H - Dummy species to track oxidation of TRO2 by HO2 - not listed - 173.16 * - LTRO2N - Dummy species to track oxidation of TRO2 by NO - not listed - 173.16 * - LXRO2H - Dummy species to track oxidation of XRO2 by HO2 - not listed - 187.19 * - LXRO2N - Dummy species to track oxidation of XRO2 by NO - not listed - 187.19 * - MACR1OO - Peroxyacyl radical from MACR + OH - CH2=C(CH3)C(O)OO - 101.09 * - MACRNO2 - Product of MCRHN + OH - C4H6NO7 - 180.1 * - MCO3 - Peroxyacetyl radical - CH3C(O)OO - 75.05 * - MCROHOO - Peroxy radical from MACR + OH - C4H7O4 - 119.11 * - MEKCO3 - not listed - C3H5O4 - 105.07 * - MO2 - Methylperoxy radical - CH3O2 - 47.04 * - MVKOHOO - Peroxy radical from MVK + OH - C4H7O4 - 119.11 * - N - Atomic nitrogen - N - 14.01 * - NAP - Naphtalene/IVOC surrogate - C10H8 - 128.18 * - NRO2 - Peroxy radical from NAP oxidation - C10H7O2 - 159.17 * - O - Ground state atomic oxygen - O(3P) - 16.0 * - O1D - Excited atomic oxygen (1D) - O(1D) - 16.0 * - OH - Hydroxyl radical - OH - 17.01 * - OLND - Monoterpene-derived NO3-alkene adduct - C10H16NO5 - 230.27 * - OLNN - Monoterpene-derived NO3 adduct - C10H16NO5 - 230.27 * - OTHRO2 - Other C2 RO2 not from C2H6 oxidation - CH3CH2OO - 61.07 * - PIO2 - Peroxy radical from MTPA - C10H17O3 - 185.27 * - PO2 - Peroxy radical from propene - HOCH2CH(OO)CH3 - 91.1 * - PRN1 - Peroxy radical from propene + NO3 - O2NOCH2CH(OO)CH3 - 136.09 * - R4N1 - Peroxy radical from R4N2 - C4H8NO5 - 150.13 * - R4O2 - Peroxy radical from isoprene and MTPA alkyl generation - C4H9O2 - 89.13 * - R7O2 - Peroxy radical from ALK6 - C7H15O2 - 131.19 * - R7N1 - Peroxy radical from R7N2 - C7H15NO5 - 161.2 * - RCO3 - Peroxypropionyl radical - CH3CH2C(O)OO - 89.08 * - ROH - > C2 alcohols - C3H7OH - 60.11 * - TLFUO2 - not listed - C5H7O5 - 147.1 * - TRO2 - Peroxy radical from TOLU oxidation - C7H9O5 - 173.16 * - XRO2 - Peroxy radical from TOLU oxidation - C8H11O5 - 187.19 * - PH2SO4 - SO4 from gas-phase chemistry - not listed - 96.06 * - PSO4AQ - SO4 from cloud chemistry - not listed - 96.06 * - ZRO2 - RO2 for making lumped aromatic nitrate - C7H9O5 - 173.16 * - H2 - Molecular hydrogen - H2 - 2.02 * - N2 - Molecular nitrogen - N2 - 28.02 * - O2 - Molecular oxygen - O2 - 32.0 .. _fullchem-sim-benchmark: Benchmark --------- Fullchem simulations with the :program:`Benchmark` option allow the `GEOS-Chem Support Team `_ to perform simulations that document the performance and evolution of GEOS-Chem over time. Benchmark simulations use all of the :ref:`Standard species `, as well as the :ref:`Complex SOA species ` listed below. However, the complex SOA species are carried solely for diagnostic purposes. .. _fullchem-sim-csoa: Complex SOA ----------- Fullchem simulations with :program:`Complex SOA` option use all of the :ref:`Standard species `, plus 15 additional transported species. .. list-table:: Additional transported species (Complex SOA) :header-rows: 1 :align: left * - Species - Description - MW (g) * - ASOA1 - Lumped non-volatile aerosol products of light aromatics + IVOCs - 150.0 * - ASOA2 - Lumped non-volatile aerosol products of light aromatics + IVOCs - 150.0 * - ASOA3 - Lumped non-volatile aerosol products of light aromatics + IVOCs - 150.0 * - ASOAN - Lumped non-volatile aerosol products of light aromatics + IVOCs - 150.0 * - ASOG1 - Lumped non-volatile gas products of light aromatics + IVOCs - 150.0 * - ASOG2 - Lumped non-volatile gas products of light aromatics + IVOCs - 150.0 * - ASOG3 - Lumped non-volatile gas products of light aromatics + IVOCs - 150.0 * - TSOA0 - Lumped semivolatile aerosol products of monoterpene + sesquiterpene oxidation - 150.0 * - TSOA1 - Lumped semivolatile aerosol products of monoterpene + sesquiterpene oxidation - 150.0 * - TSOA2 - Lumped semivolatile aerosol products of monoterpene + sesquiterpene oxidation - 150.0 * - TSOA3 - Lumped semivolatile aerosol products of monoterpene + sesquiterpene oxidation - 150.0 * - TSOG0 - Lumped semivolatile gas products of monoterpene + sesquiterpene oxidation - 150.0 * - TSOG1 - Lumped semivolatile gas products of monoterpene + sesquiterpene oxidation - 150.0 * - TSOG2 - Lumped semivolatile gas products of monoterpene + sesquiterpene oxidation - 150.0 * - TSOG3 - Lumped semivolatile gas products of monoterpene + sesquiterpene oxidation - 150.0 You may archive several complex SOA diagnostic quantities to the :ref:`AerosolMass History collection `. .. _fullchem-sim-svpoa: Complex SOA plus semi-volatile POA ---------------------------------- Fullchem simulations with :program:`Complex SOA plus semi-volatile POA` use all of the :ref:`Standard species ` and :ref:`Complex SOA species `, plus several additional transported primary organic aerosol species. .. list-table:: Additional transported species (Complex SOA with SVPOA) :header-rows: 1 :align: left * - Species - Description - MW (g) * - OPOA1 - Lumped aerosol product of SVOC oxidation - 12.01 * - OPOA2 - Lumped aerosol product of SVOC oxidation - 12.01 * - OPOG1 - Lumped gas product of SVOC oxidation - 12.01 * - OPOG2 - Lumped gas product of SVOC oxidation - 12.01 * - POA1 - Lumped aerosol primary SVOCs - 12.01 * - POA2 - Lumped aerosol primary SVOCs - 12.01 * - POG1 - Lumped gas primary SVOCs - 12.01 * - POG2 - Lumped gas primary SVOCs - 12.01 .. _fullchem-sim-mpoa: Marine POA ---------- Fullchem simulations with :program:`Marine POA` use all of the :ref:`Standard species `, plus two additional transported aerosol species. .. list-table:: Additional transported species (Marine POA) :header-rows: 1 :align: left * - Species - Description - Formula - MW (g) * - MOPI - Hydrophilic marine organic carbon aerosol - C - 12.01 * - MOPO - Hydrophobic marine organic carbon aerosol - C - 12.01 .. _fullchem-sim-aciduptake: Acid uptake on dust ------------------- Fullchem simulations with :program:`Acid uptake on dust` use all of the :ref:`Standard species `, plus 12 additional transported species. .. list-table:: Additional transported species (Acid uptake on dust) :header-rows: 1 :align: left * - Species - Description - MW (g) * - DSTALbin1 - Dust alkalinity, Reff = 0.151 :math:`\mu\text{m}` - 29.0 * - DSTALbin2 - Dust alkalinity, Reff = 0.253 :math:`\mu\text{m}` - 29.0 * - DSTALbin3 - Dust alkalinity, Reff = 0.402 :math:`\mu\text{m}` - 29.0 * - DSTALbin4 - Dust alkalinity, Reff = 0.818 :math:`\mu\text{m}` - 29.0 * - DSTALbin5 - Dust alkalinity, Reff = 1.491 :math:`\mu\text{m}` - 29.0 * - DSTALbin6 - Dust alkalinity, Reff = 2.417 :math:`\mu\text{m}` - 29.0 * - DSTALbin7 - Dust alkalinity, Reff = 3.721 :math:`\mu\text{m}` - 29.0 * - NITDbin1 - Nitrate on dust,, Reff = 0.151 :math:`\mu\text{m}` - 62.01 * - NITDbin2 - Nitrate on dust, Reff = 0.253 :math:`\mu\text{m}` - 62.01 * - NITDbin3 - Nitrate on dust, Reff = 0.402 :math:`\mu\text{m}` - 62.01 * - NITDbin4 - Nitrate on dust, Reff = 0.818 :math:`\mu\text{m}` - 62.01 * - NITDbin5 - Nitrate on dust, Reff = 1.491 :math:`\mu\text{m}` - 62.01 * - NITDbin6 - Nitrate on dust, Reff = 2.417 :math:`\mu\text{m}` - 62.01 * - NITDbin7 - Nitrate on dust, Reff = 3.721 :math:`\mu\text{m}` - 62.01 * - SO4Dbin1 - Sulfate on dust,, Reff = 0.151 :math:`\mu\text{m}` - 96.06 * - SO4Dbin2 - Sulfate on dust, Reff = 0.253 :math:`\mu\text{m}` - 96.06 * - SO4Dbin3 - Sulfate on dust, Reff = 0.402 :math:`\mu\text{m}` - 96.06 * - SO4Dbin4 - Sulfate on dust, Reff = 0.818 :math:`\mu\text{m}` - 96.06 * - SO4Dbin5 - Sulfate on dust, Reff = 1.491 :math:`\mu\text{m}` - 96.06 * - SO4Dbin6 - Sulfate on dust, Reff = 2.417 :math:`\mu\text{m}` - 96.06 * - SO4Dbin7 - Sulfate on dust, Reff = 3.721 :math:`\mu\text{m}` - 96.06 .. _fullchem-sim-tomas: TOMAS aerosol microphysics -------------------------- Fullchem simulations with :program:`TOMAS aerosol microphysics` use all of the :ref:`Standard species `, plus several additional size-resolved aerosol species. Note that the bulk dust species (DST1, DST2, DST3, DST4) species are replaced with size-resolved dust species (DUST1 .. DUST40). .. list-table:: Additional transported species (TOMAS) :header-rows: 1 :align: left * - Species - Description - MW (g) * - AW01 .. AW40 - Aerosol water, size bins 1 .. 40 - 18.0 * - DUST01 .. DUST40 - Mineral dust, size bins 1 .. 40 - 100.0 * - ECIL01 .. ECIL40 - Hydrophilic elemental carbon, size bins 1 .. 40 - 12.01 * - ECOB01 .. ECOB40 - Hydrophobic elemental carbon, size bins 1 .. 40 - 12.01 * - H2SO4: - Sulfuric acid - 98.0 * - NK01 .. NK40 - Aerosol number, size bins 1..40 - 1.0 * - OCIL01 .. OCIL40 - Hydrophilic organic carbon, size bins 1 .. 40 - 12.01 * - OCOB01 .. OCOB40 - Hydrophilic organic carbon, size bins 1 .. 40 - 12.01 * - SF01 .. SF40 - Sulfate aerosol, size bins 1 .. 40 - 96.0 * - SS01 .. SS40 - Sea salt aerosol, size bins 1 .. 40 - 58.5 You must request TOMAS aerosol microphysics at configuration time. You may select either TOMAS with 15 size-resolved bins or with 40 size-resolved bins. Please see :ref:`this section ` for configuration and compilation instructions. You may archive several TOMAS diagnostic quantities to the :ref:`TOMAS History collection `. .. _fullchem-sim-apm: APM aerosol microphysics ------------------------ Fullchem simulations with :program:`APM aerosol microphysics` use all species listed in the :ref:`fullchem-sim-standard`, as well as the following species: .. list-table:: Additional transported species (APM) :header-rows: 1 :align: left * - Species - Description - MW (g) * - APMAMINE1 - APM amines 1 - 31.0 * - APMAMINE2 - APM amines 2 - 45.0 * - APMAMINE3 - APM amines 3 - 59.0 * - APMBCBIN01 .. APMBCBIN15 - APM black carbon, size bins 01 .. 15 - 12.01 * - APMCTBC1 - APM CTSO4 - 96.0 * - APMCTBC2 - APM CTSLVSOA - 181.0 * - APMCTDST1 - APM CTSO4 - 96.0 * - APMCTDST2 - APM CTLVSOA - 181.0 * - APMCTOC1 - APM CTSO4 - 96.0 * - APMCTOC2 - APM CTLVSOA - 181.0 * - APMCTSEA1 - APM CTSO4 - 96.0 * - APMCTSEA2 - APM CTLVSOA - 181.0 * - APMDSTBIN01 .. APMDSTBIN15 - APM Dust - 29.0 * - APMH2SO4 - APM sulfuric acid - 98.0 * - APMLVSOA - APM LVSOA - 181.0 * - APMLVSOG - APM LV secondary organic gas - 181.0 * - APMOCBIN01 .. APMOCBIN15 - APM organic carbon, size bins 01 .. 15 - 12.01 * - APMSEABIN01 .. APMSEABIN20 - APM sea salt, size bins 01 .. 20 - 12.01 * - APMSPBIN01 .. APMSPBIN40 - APM sulfate, size bins 01 .. 40 - 96.0 You must request APM aerosol microphysics at configuration time. Please see :ref:`this section ` for configuration and compilation instructions. .. _fullchem-sim-rrtmg: RRTMG radiative transfer model ------------------------------ Fullchem simulations with the :program:`RRTMG radiative transfer model` use the :ref:`Standard species `. No additional species are included. Radiative forcing diagnostics can be archived to the :ref:`RRTMG History collection `.