This directory contains the files:
mm2.3           - NCAR Master Mechanism version 2.3 listing of reactions (see below)
alphadict.dat   - dictionary of 4-character species code names.
troe.mch        - Troe reaction data
shrink.f        - code to reduce size of mechanism:
                - reads desired starting species from file input.species
                - can edit to exclude certain reactions with X.
                - output is in two files:
                     tmp.mch   = new reduced chemical mechanism
                     tmp.dct   = new reduced dictionary
dep1.f          - estimates deposition first order rate constants for 
                  all species

##################    file mm2.3  #######################
The NCAR Master Mechanism, Version 2.3,
                see Madronich and Calvert, NCAR TN-333+STR 1989
                Updated by Patrice Gregoire in 1994, 
                        by Bernard Aumont in 1998, 
                        by Craig Stroud in 2002,
                        by Sasha Madronich in 2005.
                The mechanism is coded with 4-character names for 
                each chemical.  See ALPHADICT.DAT for translation to 
                full chemical formulae.
                The general format is
CFR1   R2   R3   >  s1   P1    s2   P2    s3   P3    s4   P4   k(298K)  E/R
where   C is a comment to help identify class of reaction
        F is a flag for special handling.  
                If the flag is "s", a special rate constant equation
                is used in the solver, for example for the reactions 
                        CO  +  HO
                        HNO3 + OH
                        HO2 + HO2
        R1, R2, and R3 are the reagents (4 characters max)
        > is the reaction arrow.  When reactions are split because they have more than
                four products, the > is replaced by "1", "2", etc. and the stoichiometry 
                coefficients and rate constants are adjusted accordingly.  This adjustment
                is as follows:  If the reaction is split into n reactions, each stoichiometry
                coefficient of the products should be multiplied by n, and the rate constant
                divided by n.  For example, the reaction R -> A+B+C+D+E+F , rate constant k, can be
                rewritten as the pair of reactions 
		    R -> 2A + 2B + 2C, k/2   and
                    R -> 2E + 2F,  k/2.
        > is followed by a letter, e.g.: >A  or >B, when there are multiple channels, A and B
                in this example.  This is different than splitting reactions because it allows
                different rate constants and temperature dependencies. 
        s1, s2, s3, s4 are the product stoichiometry coefficients.
        P1, P2, P3, P4 are the product species
        k(298K) is the rate constant at 760 torr, 298K
        E/R is the activation temperature (Kelvin), in the Arrhenius sense.  For Troe
                and special reactions, it is the local (298K, 760 Torr) tangent of 
                the Arrhenius plot
Most reactions are in simple Arrhenius form.  Exceptions are:
Photolysis reactions:  one of the reagents is HV (photon flag), and the rate constant
        is listed as 1.0E-36 (simply a flag).  Separate calculation of J values is
        done by other codes (not given here).
True three-body reactions have "M" as a reagent
Troe reactions have "(M)" as a reagent.  See file TROE.MCH
Reactions with "s" in column 2 have special equation for rate constant (not given here)

#######################   file  alphadict.dat   #######################
dictionary of coded chemical names.  Example:
1k51  5  0  9  0  4  0  CH2(OH)COC(O.)(CH3)CH2(OH)              | o1.ko        
Columns 1-4 give the coded name.  The six integers which follow are the
number of atoms of carbon, halogens, hydrogen, nitrogen, oxygen, and sulfur.
Next is the full chemical formula.  After the "|", given are the codes for the 
relevant functional groups.  The meaning of the codes is as follows:
Numbers are radical groups
        0 = alkyl radicals
        1 = alkoxy radicals
        2 = alkyl peroxy radicals
        3 = acyl peroxy radicals
        4 = criegee
        5-9 = misc.
Lower case letters are non-radical functional groups:
        a = Acids
        b = Bromine
        c = pure hydroCarbon
        d = alDehydes
        e = Ethers, Esters
        f = Fluorine
        g = peroxy acids -CO(OOH)
        h = Hydroperoxides
        k = Ketones
        l = chLorine
        m = amine
        n = org. nitrates
        o = alcOhol
        p = Peroxy acyl nitrates (PAN and the like)
        q = misc inorganic
        s = sulfur
        t = alpha-pinene and its derivatives
        u = double bond (Unsaturated )
        v = nitro (-NO2)
        w = nitrite (-NO)
        z = non-specific hydrocarbons, e.g., C5H12
The names are constructed as follows:
        1.  If name can be expressed unambiguously with <= 4 characters,
            it is written explicitly, e.g., CH4   HNO3   HO
        2.  If not, 
            the 1st character is the code for the most reactive functional group.
            the 2nd character is the code for the 2nd most reactive functional group.
            the 3rd character is the number of carbon atmos
            the 4th character is used to distinguish between species having the
                        same first three characters.

#######################  file troe.mch     #######################
troe coefficients for reactions which have a "(M)"

#######################   file shrink.f     #######################
fortran code to select subsets of mechanism.  Fairly obvious to use:
        set the desired starting species in file example.species
        Four species are already hard-wired in the code:  
        (blank)
        HV
        M
        (M)


        
