Changes needed to run in CH4only mode on docker

README.md

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+# Deprecated
+
+This repository has been deprecated in favour of https://github.com/openmethane/CMAQ,
+which has includes many of the same changes, but has a clearer lineage to official
+CMAQ v5.0.2.
+
+# CMAQ v5.0.2
+
+US EPA Community Multiscale Air Quality Model (CMAQ) Website: https://www.epa.gov/cmaq
+
+## Open Methane fork
+
+This repository is a version of https://github.com/USEPA/CMAQ/tree/5.0.2 which
+has been modified specifically to work for Open Methane.
+
+If you are seeking to start a new project based on CMAQ, you should use the
+official versions provided by the US EPA.

license.md

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+# MIT License
+
+Copyright (c) 2019  U.S. Federal Government (in countries where recognized)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

models/BCON/prof_data/CH4only/bc_profile_CH4only.dat

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+ CB05 gas mechanism with AERO5 species and toxics
+ bcon profile data converted from RADM2 gas mechanism species
+  layers and defined sigma levels are listed below.
+    6  1     1.00  0.98  0.93  0.84  0.60  0.30  0.00
+ 2011-08-10
+  North
+"CH4             "   1.8       1.8       1.8       1.8       1.8       1.8    
+  East 
+"CH4             "   1.8       1.8       1.8       1.8       1.8       1.8    
+  South
+"CH4             "   1.8       1.8       1.8       1.8       1.8       1.8    
+  West 
+"CH4             "   1.8       1.8       1.8       1.8       1.8       1.8    

models/CCTM/MECHS/CH4only/AE_CH4only.csv

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+SPC,MOLWT,EMIS_SUR,EMIS_FAC,DEPV_SUR,DEPV_FAC,SCAV_SUR,SCAV_FAC,ICBC_SUR,ICBC_FAC,A2AQ_SUR,TRNS,DDEP,WDEP,CONC

models/CCTM/MECHS/CH4only/AE_CH4only.nml

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+! RCS file, release, date & time of last delta, author, state, [and locker]
+! $Header: /project/yoj/arc/MECHS/src/cb05cl_ae5_aq/AE_cb05cl_ae5_aq.nml,v 1.1 2011/12/09 11:49:56 yoj Exp $
+
+&AE_nml
+
+n_surr1 = 4,
+n_surr2 = 1,
+n_ctrl = 4,
+
+TYPE_HEADER =
+'SPC:MOLWT:EMIS_SUR:EMIS_FAC:DEPV_SUR:DEPV_FAC:SCAV_SUR:SCAV_FAC:ICBC_SUR:ICBC_FAC:A2AQ_SUR:TRNS:DDEP:WDEP:CONC',
+TYPE_MATRIX =
+/

models/CCTM/MECHS/CH4only/GC_CH4only.csv

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+SPC,MOLWT,EMIS_SUR,EMIS_FAC,DEPV_SUR,DEPV_FAC,ICBC_SUR,ICBC_FAC,SCAV_SUR,SCAV_FAC,G2AE_SUR,G2AQ_SUR,TRNS,DDEP,WDEP,CONC
+CH4,16.0,CH4,1.0,,,CH4,1.0,,,,,Yes,,,Yes

models/CCTM/MECHS/CH4only/GC_CH4only.nml

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+! RCS file, release, date & time of last delta, author, state, [and locker]
+! $Header: /project/yoj/arc/MECHS/src/cb05cl_ae5_aq/GC_cb05cl_ae5_aq.nml,v 1.1 2011/12/09 11:49:57 yoj Exp $
+
+&GC_nml
+
+n_surr1 = 4,
+n_surr2 = 2,
+n_ctrl = 4,
+
+TYPE_HEADER =
+'SPC:MOLWT:EMIS_SUR:EMIS_FAC:DEPV_SUR:DEPV_FAC:ICBC_SUR:ICBC_FAC:SCAV_SUR:SCAV_FAC:G2AE_SUR:G2AQ_SUR:TRNS:DDEP:WDEP:CONC',
+TYPE_MATRIX =
+'CH4:16.0:CH4:1.0::1.0:CH4:1.0:::::Yes:No:No:Yes',
+/

models/CCTM/MECHS/CH4only/NR_CH4only.csv

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+SPC,MOLWT,EMIS_SUR,EMIS_FAC,DEPV_SUR,DEPV_FAC,ICBC_SUR,ICBC_FAC,SCAV_SUR,SCAV_FAC,N2AE_SUR,N2AQ_SUR,TRNS,DDEP,WDEP,CONC

models/CCTM/MECHS/CH4only/NR_CH4only.nml

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+! RCS file, release, date & time of last delta, author, state, [and locker]
+! $Header: /project/yoj/arc/MECHS/src/cb05cl_ae5_aq/NR_cb05cl_ae5_aq.nml,v 1.1 2011/12/09 11:49:57 yoj Exp $
+
+&NR_nml
+
+n_surr1 = 4,
+n_surr2 = 2,
+n_ctrl = 4,
+
+TYPE_HEADER =
+'SPC:MOLWT:EMIS_SUR:EMIS_FAC:DEPV_SUR:DEPV_FAC:ICBC_SUR:ICBC_FAC:SCAV_SUR:SCAV_FAC:N2AE_SUR:N2AQ_SUR:TRNS:DDEP:WDEP:CONC',
+TYPE_MATRIX =
+/

models/CCTM/MECHS/CH4only/RXCM.EXT

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+
+C RCS file, release, date & time of last delta, author, state, [and locker]
+C $Header: /project/yoj/arc/MECHS/src/cb05cl_ae5_aq/RXCM.EXT,v 1.2 2011/03/24 16:15:48 sjr Exp $
+
+C what(1) key, module and SID; SCCS file; date and time of last delta:
+C %W% %P% %G% %U%
+
+C -------- Mechanism Reactions, Rates, etc. COMMON INCLUDE File --------
+C  /home/hutzellb/cmaq_toxics/releases_2010/new_arc_mechanisms
+C  /cb05cl_ae5_aq/RXCM.EXT
+C for Mechanism Name: CB05CL_AE5_AQ                   
+
+C The following are reserved symbols declared in this INCLUDE file:
+C    MECHNAME       = Mechanism name
+C    N_GAS_CHEM_SPC = Total number of species in gas phase chemical mechanism
+C    N_ACT_SP       = Number of active (determined by ODE solver) species in mechanism
+C    NRXNS          = Number of mechanism reactions
+C    KUNITS         = Units of mechanism reactions
+C    KTYPE          = Reaction type
+C    IRXBITS        = Bit test mask vector for selected reactions
+C    IORDER         = Order of the reaction
+C    KTN1           = Number of type 1 reactions
+C    KRX1           = Reactions list pointer to type 1 reactions
+C    KTN2           = Number of type 2 reactions
+C    KRX2           = Reactions list pointer to type 2 reactions
+C    KTN3           = Number of type 3 reactions
+C    KRX3           = Reactions list pointer to type 3 reactions
+C    KTN4           = Number of type 4 reactions
+C    KRX4           = Reactions list pointer to type 4 reactions
+C    KTN5           = Number of type 5 reactions
+C    KRX5           = Reactions list pointer to type 5 reactions
+C    KTN6           = Number of type 6 reactions
+C    KRX6           = Reactions list pointer to type 6 reactions
+C    KTN7           = Number of type 7 reactions
+C    KRX7           = Reactions list pointer to type 7 reactions
+
+C    NWM       = Number of air 3-body reactions
+C    NRXWM     = Reactions list pointer to air 3-body reactions
+C    ATM_AIR   = air 3-body reactions concentration
+C    NWW       = Number of H2O 3-body reactions
+C    NRXWW     = Reactions list pointer to H2O 3-body reactions
+C    NWO2      = Number of reactions with O2
+C    NRXWO2    = Reactions list pointer to O2 reactions
+C    ATM_O2    = Oxygen reactions concentration
+C    NWN2      = Number of N2 3-body reactions
+C    NRXWN2    = Reactions list pointer to N2 3-body reactions
+C    ATM_N2    = Nitrogen 3-body reactions concentration
+C    NWCH4     = Number of reactions with CH4
+C    NRXWCH4   = Reactions list pointer to CH4 reactions
+C    ATM_CH4   = Methane reactions concentration
+C    NWH2      = Number of reactions with H2
+C    NRXWH2    = Reactions list pointer to H2 reactions
+C    ATM_H2    = Hydrogen reactions concentration
+
+C    MXPRD     = Maximum number of mechanism reaction products
+C    IRR       = Reactions list pointer to reactants and products
+C    RTDAT     = Kinetic reaction rates expressions components
+C    NFALLOFFF = Number of falloff reactions
+C    IRRFALL   = Reactions list pointer to falloff reactions
+C    RFDAT     = Falloff reaction rates expressions components
+C    SC        = Stoichiometric coefficients
+C    NREACT    = Number of reactants in each mechanism reaction
+C    NPRDCT    = Number of products in each mechanism reaction
+C    RXLABEL   = Character label list for mechanism reactions
+C    NMPHOT    = Number of mechanism photolytic reactions
+C    NPHOTAB   = Number of photolytic reactions tables
+C    IPH       = Reactions list pointer to photolytic reactions and tables
+
+      CHARACTER( 32 ), PARAMETER :: MECHNAME = 'CH4only'
+
+      INTEGER, PARAMETER :: N_GAS_CHEM_SPC =  1
+
+      INTEGER, PARAMETER :: N_ACT_SP =  1
+
+      INTEGER, PARAMETER :: NRXNS = 1
+
+      INTEGER            :: KUNITS
+
+      INTEGER            :: KTYPE( NRXNS )
+
+      INTEGER            :: IRXBITS( NRXNS )
+
+      INTEGER            :: IORDER( NRXNS )
+
+      INTEGER, PARAMETER :: KTN1 =  1
+      INTEGER            :: KRX1( KTN1 )
+
+      INTEGER, PARAMETER :: KTN2 =   1
+      INTEGER            :: KRX2( KTN2 )
+
+      INTEGER, PARAMETER :: KTN3 =  1
+      INTEGER            :: KRX3( KTN3 )
+
+      INTEGER, PARAMETER :: KTN4 =   1
+      INTEGER            :: KRX4( KTN4 )
+
+      INTEGER, PARAMETER :: KTN5 =   0
+      INTEGER            :: KRX5( 1 )
+
+      INTEGER, PARAMETER :: KTN6 =   0
+      INTEGER            :: KRX6( 1 )
+
+      INTEGER, PARAMETER :: KTN7 =   0
+      INTEGER            :: KRX7( 1 )
+
+      INTEGER, PARAMETER :: NWM =   2
+      INTEGER            :: NRXWM( NWM )
+      REAL,    PARAMETER :: ATM_AIR = 1.00000E+06
+
+      INTEGER, PARAMETER :: NWW =   6
+      INTEGER            :: NRXWW( NWW )
+
+      INTEGER, PARAMETER :: NWO2 =   2
+      INTEGER            :: NRXWO2( NWO2 )
+      REAL,    PARAMETER :: ATM_O2 = 2.09500E+05
+
+      INTEGER, PARAMETER :: NWN2 =   0
+      INTEGER            :: NRXWN2( 1 )
+      REAL,    PARAMETER :: ATM_N2 = 7.80800E+05
+
+      INTEGER, PARAMETER :: NWCH4 =   2
+      INTEGER            :: NRXWCH4( NWCH4 )
+      REAL,    PARAMETER :: ATM_CH4 = 1.85000E+00
+
+      INTEGER, PARAMETER :: NWH2 =   2
+      INTEGER            :: NRXWH2( NWH2 )
+      REAL,    PARAMETER :: ATM_H2 = 5.60000E-01
+
+      INTEGER, PARAMETER :: MXPRD =  10
+      INTEGER            :: IRR( NRXNS,MXPRD+3 )
+
+      INTEGER, PARAMETER :: NFALLOFF =  19
+      INTEGER            :: IRRFALL( NFALLOFF )
+
+      REAL               :: SC( NRXNS,MXPRD )
+
+      INTEGER            :: NREACT( NRXNS )
+      INTEGER            :: NPRDCT( NRXNS )
+
+      INTEGER, PARAMETER :: NMPHOT =  26
+      INTEGER            :: IPH( NMPHOT,3 )
+
+      COMMON     / MECHRX1 /
+     &             KUNITS,
+     &             KTYPE,
+     &             IRXBITS,
+     &             IORDER,
+     &             KRX1,
+     &             KRX2,
+     &             KRX3,
+     &             KRX4,
+     &             KRX7,
+     &             KRX5,
+     &             KRX6,
+     &             NRXWM,
+     &             NRXWW,
+     &             NRXWO2,
+     &             NRXWN2,
+     &             NRXWCH4,
+     &             NRXWH2,
+     &             IRR,
+     &             IRRFALL,
+     &             SC,
+     &             NREACT,
+     &             NPRDCT,
+     &             IPH
+
+      REAL( 8 )          :: RTDAT( 3,NRXNS )
+      REAL( 8 )          :: RFDAT( 5,NFALLOFF )
+
+      COMMON     / MECHRX2 /
+     &             RTDAT,
+     &             RFDAT
+
+      INTEGER, PARAMETER :: NPHOTAB =  23
+      CHARACTER( 16 )    :: PHOTAB( NPHOTAB )
+
+      CHARACTER( 16 )    :: RXLABEL( NRXNS )
+
+      COMMON     / MECHRX3 /
+     &             PHOTAB,
+     &             RXLABEL
+
+C End of Mechanism Reactions, Rates, etc. COMMON INCLUDE File ----------
+
+C    NSPECIAL     = Number of special rate coefficients
+C    SPECIAL      = Names of special rate coefficients
+C    NSPECIAL_RXN = Number of reactions with special rates
+C    ISPECIAL     = Pointers to reactions using special rates and their special rate coefficients
+C    MAXSPECTERMS = Max Number of each term type in  special rate coefficients
+C    KC_COEFFS    = Coefficients of standard rate coefficients  times concentration terms 
+C    INDEX_KTERMS  = Pointers to standard rate coefficients in  special rate coefficients
+C    INDEX_CTERMS  = Pointers to species concentrations in  special rate coefficients
+C    OPERATOR_COEFFS = Coefficients of preceeding special  rate coefficients used in special coefficient 
+C    OPERATORS       = Pointers to preceeding special  rate coefficients used in special coefficient 
+
+C Special Rate information not available ..
+      INTEGER, PARAMETER :: NSPECIAL_RXN = 0
+      INTEGER            :: ISPECIAL( 1, 2 )
+
+C Special Rate information not available ...
+      INTEGER, PARAMETER :: NSPECIAL = 0
+
+C Special Rate information not available ...
+      CHARACTER( 16 )    :: SPECIAL( 1 )
+
+      INTEGER, PARAMETER :: MAXSPECTERMS =  10
+      REAL( 8 )          :: KC_COEFFS( NSPECIAL + 1, MAXSPECTERMS)
+      INTEGER            :: INDEX_KTERMS( NSPECIAL + 1, MAXSPECTERMS)
+      INTEGER            :: INDEX_CTERMS( NSPECIAL + 1, MAXSPECTERMS)
+      REAL( 8 )          :: OPERATOR_COEFFS( NSPECIAL + 1, MAXSPECTERMS)
+      INTEGER            :: OPERATORS( NSPECIAL + 1, MAXSPECTERMS)
+
+      COMMON     / MECHRX4 /
+     &             SPECIAL,
+     &             ISPECIAL,
+     &             KC_COEFFS,
+     &             INDEX_KTERMS,
+     &             INDEX_CTERMS,
+     &             OPERATOR_COEFFS,
+     &             OPERATORS
+
+
+C    Steady-state species section
+C    N_SS_SPC     = Number of species assumed to be in steady-state
+C    SS_SPC_DIM   = Dimension paramete for steady-state species
+C    SS_SPC       = Names of species assumed to be in steady-state
+C    MAX_SS_LOSS  = Max no. of SS loss rxns for any SS species
+C    MAX_SS_PROD  = Max no. of SS prod rxns for any SS species
+C    N_LOSS_RXNS  = No. of SS loss rxns for each SS species
+C    N_PROD_RXNS  = No. of SS prod rxns for each SS species
+C    SS_LOSS_RXNS = List of SS loss rxns for each SS species
+C    SS_PROD_RXNS = List of SS prod rxns for each SS species
+C    SS_PROD_COEF = List of SS prod yields for each SS species
+C    SS_RCT_IND   = SS species index if it is a rxn reactant
+
+      INTEGER, PARAMETER :: N_SS_SPC =   0
+
+      INTEGER, PARAMETER :: SS_SPC_DIM =   1
+
+      INTEGER, PARAMETER :: MAX_SS_LOSS =   0
+
+      INTEGER, PARAMETER :: MAX_SS_PROD =   0
+
+      CHARACTER( 16 )    :: SS_SPC( 1 )
+
+      INTEGER            :: N_LOSS_RXNS( 1 )
+      INTEGER            :: N_PROD_RXNS( 1 )
+      INTEGER            :: SS_LOSS_RXNS( 1, 1 )
+      INTEGER            :: SS_PROD_RXNS( 1, 1 )
+      INTEGER            :: SS_RCT_IND( 1 )
+
+      REAL               :: SS_PROD_COEF( 1,1 ) 
+
+      COMMON     / MECHRX5 /
+     &             SS_SPC,
+     &             N_LOSS_RXNS,
+     &             N_PROD_RXNS,
+     &             SS_LOSS_RXNS,
+     &             SS_PROD_RXNS,
+     &             SS_PROD_COEF,
+     &             SS_RCT_IND