# Update chemical mechanisms with KPP¶

This Guide demonstrates how you can use The Kinetic PreProcessor (aka KPP) to translate a chemical mechanism specification in plain text format to highly-optimized Fortran90 code for use with GEOS-Chem:

## Using KPP: Quick start¶

### 2. Edit the chemical mechanism configuration files¶

The KPP/custom folder contains sample chemical mechanism specification files (custom.eqn and custom.kpp). These files define the chemical mechanism and are copies of the default fullchem mechanism configuration files found in the KPP/fullchem folder. (For a complete description of KPP configuration files, please see the documentation at kpp.readthedocs.io.)

You can edit these custom.eqn and custom.kpp configuration files to define your own custom mechanism (cf. Using KPP: Reference section for details).

Important

We recommend always building a custom mechanism from the KPP/custom folder, and to leave the other folders untouched. This will allow you to validate your modified mechanism against one of the standard mechanisms that ship with GEOS-Chem.

#### custom.eqn¶

The custom.eqn configuration file contains:

• List of active species

• List of inactive species

• Gas-phase reactions

• Heterogeneous reactions

• Photolysis reactions

#### custom.kpp¶

The custom.kpp configuration file is the main configuration file. It contains:

• Solver options

• Production and loss family definitions

• Functions to compute reaction rates

• Global definitions

• An #INCLUDE custom.eqn command, which tells KPP to look for chemical reaction definitions in custom.eqn.

Important

The symbolic link gckpp.kpp points to custom.kpp. This is necessary in order to generate Fortran files with the the naming convention gckpp*.F90.

### 3. Run the build_mechanism.sh script¶

Once you are satisfied with your custom mechanism specification you may now use KPP to build the source code files for GEOS-Chem.

Return to the top-level KPP folder from KPP/custom:

$cd ..  There you will find a script named build_mechanism.sh, which is the driver script for running KPP. Execute the script as follows: $ ./build_mechanism.sh custom


This will run the KPP executable (located in the folder $KPP_HOME/bin) custom.kpp configuration file (via symbolic link gckpp.kpp, It also runs a python script to generate code for the OH reactivity diagnostic. You should see output similar to this: This is KPP-X.Y.Z. KPP is parsing the equation file. KPP is computing Jacobian sparsity structure. KPP is starting the code generation. KPP is initializing the code generation. KPP is generating the monitor data: - gckpp_Monitor KPP is generating the utility data: - gckpp_Util KPP is generating the global declarations: - gckpp_Main KPP is generating the ODE function: - gckpp_Function KPP is generating the ODE Jacobian: - gckpp_Jacobian - gckpp_JacobianSP KPP is generating the linear algebra routines: - gckpp_LinearAlgebra KPP is generating the utility functions: - gckpp_Util KPP is generating the rate laws: - gckpp_Rates KPP is generating the parameters: - gckpp_Parameters KPP is generating the global data: - gckpp_Global KPP is generating the driver from none.f90: - gckpp_Main KPP is starting the code post-processing. KPP has succesfully created the model "gckpp". Reactivity consists of 172 reactions Written to gckpp_Util.F90  where X.Y.Z denotes the KPP version that you are using. If this process is successful, the custom folder will have several new files starting with gckpp: $ ls gckpp*
gckpp_Function.F90    gckpp_Jacobian.F90       gckpp.map             gckpp_Precision.F90
gckpp_Global.F90      gckpp_JacobianSP.F90     gckpp_Model.F90       gckpp_Rates.F90
gckpp_Initialize.F90  gckpp.kpp@               gckpp_Monitor.F90     gckpp_Util.F90
gckpp_Integrator.F90  gckpp_LinearAlgebra.F90  gckpp_Parameters.F90


The gckpp*.F90 files contain optimized Fortran-90 instructions for solving the chemical mechanism that you have specified. The gckpp.map file is a human-readable description of the mechanism. Also, gckpp.kpp is a symbolic link to the custom.kpp file.

A complete description of these KPP-generated files at kpp.readthedocs.io.

### 4. Recompile GEOS-Chem with your custom mechanism¶

GEOS-Chem will always use the default mechanism (which is named fullchem). To tell GEOS-Chem to use the custom mechanism instead, follow these steps.

Tip

GEOS-Chem Classic run directories have a subdirectory named build in which you can configure and build GEOS-Chem. If you don’t have a build directory, you can add one to your run directory with mkdir build.

From the build directory, type:

$cmake ../CodeDir -DMECH=custom -DRUNDIR=..  You should see output similar to this written to the screen: -- General settings: * CUSTOMMECH: fullchem Hg **custom**  This confirms that the custom mechanism has been selected. Once you have configured GEOS-Chem to use the custom mechanism, you may build the exectuable. Type: $ make -j
\$ make -j install


The executable file (gcclassic or gchp, depending on which mode of GEOS-Chem that you are using) will be placed in the run directory.

## Using KPP: Reference section¶

### Adding species to a mechanism¶

List chemically-active (aka variable) species in the #DEFVAR section of custom.eqn, as shown below:

#DEFVAR
A3O2       = IGNORE; {CH3CH2CH2OO; Primary RO2 from C3H8}
ACET       = IGNORE; {CH3C(O)CH3; Acetone}
ACTA       = IGNORE; {CH3C(O)OH; Acetic acid}
...etc ...


The IGNORE tells KPP not to perform mass-balance checks, which would make GEOS-Chem execute more slowly.

List species whose concentrations do not change in the #DEFFIX section of custom.eqn, as shown below:

#DEFFIX
H2         = IGNORE; {H2; Molecular hydrogen}
N2         = IGNORE; {N2; Molecular nitrogen}
O2         = IGNORE; {O2; Molecular oxygen}
... etc ...


Species may be listed in any order, but we have found it convenient to list them alphabetically.

### Adding reactions to a mechanism¶

#### Gas-phase reactions¶

List gas-phase reactions first in the #EQUATIONS section of custom.eqn.

#EQUATIONS
//
// Gas-phase reactions
//
//
O3 + NO = NO2 + O2 :                         GCARR(3.00E-12, 0.0, -1500.0);
O3 + OH = HO2 + O2 :                         GCARR(1.70E-12, 0.0, -940.0);
O3 + HO2 = OH + O2 + O2 :                    GCARR(1.00E-14, 0.0, -490.0);
O3 + NO2 = O2 + NO3 :                        GCARR(1.20E-13, 0.0, -2450.0);
... etc ...


#### Gas-phase reactions: General form¶

No matter what reaction is being added, the general procedure is the same. A new line must be added to custom.eqn of the following form:

A + B = C + 2.000D : RATE_LAW_FUNCTION(ARG_A, ARG_B ...);


The denotes the reactants ($$A$$ and $$B$$) as well as the products ($$C$$ and $$D$$) of the reaction. If exactly one molecule is consumed or produced, then the factor can be omitted; otherwise the number of molecules consumed or produced should be specified with at least 1 decimal place of accuracy. The final section, between the colon and semi-colon, specifies the function RATE_LAW_FUNCTION and its arguments which will be used to calculate the reaction rate constant k. Rate-law functions are specified in the custom.kpp file.

For an equation such as the one above, the overall rate at which the reaction will proceed is determined by $$k[A][B]$$. However, if the reaction rate does not depend on the concentration of $$A$$ or $$B$$, you may write it with a constant value, such as:

A + B = C + 2.000D : 8.95d-17


This will save the overhead of a function call.

#### Rates for two-body reactions according to the Arrhenius law¶

For many reactions, the calculation of k follows the Arrhenius law:

k = a0 * ( 300 / TEMP )**b0 * EXP( c0 / TEMP )


Important

In relation to Arrhenius parameters that you may find in scientific literature, $$a_0$$ represents the $$A$$ term and $$c_0$$ represents $$-E/R$$ (not $$E/R$$, which is usually listed).

For example, the JPL chemical data evaluation), (Feb 2017) specifies that the reaction O3 + NO produces NO2 and O2, and its Arrhenius parameters are $$A$$ = 3.0x10^-12 and $$E/R$$ = 1500. To use the Arrhenius formulation above, we must specify $$a_0 = 3.0e-12$$ and $$c_0 = -1500$$.

To specify a two-body reaction whose rate follows the Arrhenius law, you can use the GCARR rate-law function, which is defined in gckpp.kpp. For example, the entry for the $$O3 + NO = NO2 + O2$$ reaction can be written as in custom.eqn as:

O3 + NO = NO2 + O2 : GCARR(3.00E12, 0.0, -1500.0);


#### Other rate-law functions¶

The gckpp.kpp file contains other rate law functions, such as those required for three-body, pressure-dependent reactions. Any rate function which is to be referenced in the custom.eqn file must be available in gckpp.kpp prior to building the reaction mechanism.

#### Making your rate law functions computationally efficient¶

We recommend writing your rate-law functions so as to avoid explicitly casting variables from REAL*4 to REAL*8. Code that looks like this:

REAL, INTENT(IN) :: A0, B0, C0
rate = DBLE(A0) + ( 300.0 / TEMP )**DBLE(B0) + EXP( DBLE(C0)/ TEMP )


Can be rewritten as:

REAL(kind=dp), INTENT(IN) :: A0, B0, C0
rate = A0 + ( 300.0d0 / TEMP )**B0 + EXP( C0/ TEMP )


Not only do casts lead to a loss of precision, but each cast takes a few CPU clock cycles to execute. Because these rate-law functions are called for each cell in the chemistry grid, wasted clock cycles can accumulate into a noticeable slowdown in execution.

You can also make your rate-law functions more efficient if you rewrite them to avoid computing terms that evaluate to 1. We saw above (cf. Rates for two-body reactions according to the Arrhenius law) that the rate of the reaction $$O3 + NO = NO2 + O2$$ can be computed according to the Arrhenius law. But because b0 = 0, term (300/TEMP)**b0 evaluates to 1. We can therefore rewrite the computation of the reaction rate as:

k = 3.0x10^-12 + EXP( 1500 / TEMP )


Tip

The EXP() and ** mathematical operations are among the most costly in terms of CPU clock cycles. Avoid calling them whenever necessary.

A recommended implementation would be to create separate rate-law functions that take different arguments depending on which parameters are nonzero. For example, the Arrhenius law function GCARR can be split into multiple functions:

1. GCARR_abc(a0, b0, c0): Use when a0 > 0 and b0 > 0 and c0 > 0

2. GCARR_ab(a0, b0): Use when a0 > 0 and b0 > 0

3. GCARR_ac(a0, c0): Use when a0 > 0 and c0 > 0

Thus we can write the O3 + NO reaction in custom.eqn as:

O3 + NO = NO2 + O2 : GCARR_ac(3.00d12, -1500.0d0);


using the rate law function for when both a0 > 0 and c0 > 0.

### Heterogeneous reactions¶

TODO Remove reference to HET array

List heterogeneous reactions after all of the gas-phase reactions in custom.eqn, according to the format below:

//
// Heterogeneous reactions
//
HO2 = O2 :                                   HET(ind_HO2,1);                      {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE}
NO2 = 0.500HNO3 + 0.500HNO2 :                HET(ind_NO2,1);
NO3 = HNO3 :                                 HET(ind_NO3,1);
NO3 = NIT :                                  HET(ind_NO3,2);                      {2018/03/16; XW}
... etc ...


Implementing new heterogeneous chemistry requires an additional step. For the reaction in question, a reaction should be added as usual, but this time the rate function should be given as an entry in the HET array. A simple example is uptake of HO2, specified as

HO2 = O2 : HET(ind_HO2,1);


Note that the product in this case, O2, is actually a fixed species, so no O2 will actually be produced. O2 is used in this case only as a dummy product to satisfy the KPP requirement that all reactions have at least one product. Here, HET is simply an array of pre-calculated rate constants. The rate constants in HET are actually calculated in gckpp_HetRates.F90.

To implement an additional heterogeneous reaction, the rate calculation must be added to this file. The following example illustrates a (fictional) heterogeneous mechanism which converts the species XYZ into CH2O. This reaction is assumed to take place on the surface of all aerosols, but not cloud droplets (this requires additional steps not shown here). Three steps would be required:

1. Add a new line to the custom.eqn file, such as XYZ = CH2O : HET(ind_XYZ,1);

2. Add a new function to gckpp_HetRates.F90 designed to calculate the heterogeneous reaction rate. As a simple example, we can copy the function HETNO3 and rename it HETXYZ. This function accepts two arguments: molecular mass of the impinging gas-phase species, in this case XYZ, and the reaction’s “sticking coefficient” - the probability that an incoming molecule will stick to the surface and undergo the reaction in question. In the case of HETNO3, it is assumed that all aerosols will have the same sticking coefficient, and the function returns a first-order rate constant based on the total available aerosol surface area and the frequency of collisions

3. Add a new line to the function SET_HET in gckpp_HetRates.F90 which calls the new function with the appropriate arguments and passes the calculated constant to HET. Example: assuming a molar mass of 93 g/mol, and a sticking coefficient of 0.2, we would write HET(ind_XYZ, 1) = HETXYZ(93.0_fp, 0.2_fp)

The function HETXYZ can then be specialized to distinguish between aerosol types, or extended to provide a second-order reaction rate, or whatever the user desires.

### Photolysis reactions¶

List photolysis reactions after the heterogeneous reactions, as shown below.

//
// Photolysis reactions
//
O3 + hv = O + O2 :                           PHOTOL(2);      {2014/02/03; Eastham2014; SDE}
O3 + hv = O1D + O2 :                         PHOTOL(3);      {2014/02/03; Eastham2014; SDE}
O2 + hv = 2.000O :                           PHOTOL(1);      {2014/02/03; Eastham2014; SDE}
... etc ...
NO3 + hv = NO2 + O :                         PHOTOL(12);     {2014/02/03; Eastham2014; SDE}
... etc ...


A photolysis reaction can be specified by giving the correct index of the PHOTOL array. This index can be determined by inspecting the file FJX_j2j.dat.

Tip

See the photolysis section of :file:geoschem_config.yml to determine the folder in which FJX_j2j.dat is located.

For example, one branch of the $$NO_3$$ photolysis reaction is specified in the custom.eqn file as

NO3 + hv = NO2 + O : PHOTOL(12)


Referring back to FJX_j2j.dat shows that reaction 12, as specified by the left-most index, is indeed $$NO_3 = NO2 + O$$:

12 NO3       PHOTON    NO2       O                       0.886 /NO3   /


If your reaction is not already in FJX_j2j.dat, you may add it there. You may also need to modify FJX_spec.dat (in the same folder ast FJX_j2j.dat) to include cross-sections for your species. Note that if you add new reactions to FJX_j2j.dat you will also need to set the parameter JVN_ in GEOS-Chem module Headers/CMN_FJX_MOD.F90 to match the total number of entries.

If your reaction involves new cross section data, you will need to follow an additional set of steps. Specifically, you will need to:

1. Estimate the cross section of each wavelength bin (using the correlated-k method), and

2. Add this data to the FJX_spec.dat file.

For the first step, you can use tools already available on the Prather research group website. To generate the cross-sections used by Fast-JX, download the file UCI_fastJ_addX_73cx.tar.gz. You can then simply add your data to FJX_spec.dat and refer to it in FJX_j2j.dat as specified above. The following then describes how to generate a new set of cross-section data for the example of some new species MEKR:

To generate the photolysis cross sections of a new species, come up with some unique name which you will use to refer to it in the FJX_j2j.dat and FJX_spec.dat files - e.g. MEKR. You will need to copy one of the addX_*.f routines and make your own (say, addX_MEKR.f). Your edited version will need to read in whatever cross section data you have available, and you’ll need to decide how to handle out-of-range information - this is particularly crucial if your cross section data is not defined in the visible wavelengths, as there have been some nasty problems in the past caused by implicitly assuming that the XS can be extrapolated (I would recommend buffering your data with zero values at the exact limits of your data as a conservative first guess). Then you need to compile that as a standalone code and run it; this will spit out a file fragment containing the aggregated 18-bin cross sections, based on a combination of your measured/calculated XS data and the non-contiguous bin subranges used by Fast-JX. Once that data has been generated, just add it to FJX_spec.dat and refer to it as above. There are examples in the addX files of how to deal with variations of cross section with temperature or pressure, but the main takeaway is that you will generate multiple cross section entries to be added to FJX_spec.dat with the same name.

Important

If your cross section data varies as a function of temperature AND pressure, you need to do something a little different. The acetone XS documentation shows one possible way to handle this; Fast-JX currently interpolates over either T or P, but not both, so if your data varies over both simultaneously then this will take some thought. The general idea seems to be that one determines which dependence is more important and uses that to generate a set of 3 cross sections (for interpolation), assuming values for the unused variable based on the standard atmosphere.

### Adding production and loss families to a mechanism¶

Certain common families (e.g. $$PO_x$$, $$LO_x$$) have been pre-defined for you. You will find the family definitions near the top of the gckpp.kpp file:

#FAMILIES
POx : O3 + NO2 + 2NO3 + PAN + PPN + MPAN + HNO4 + 3N2O5 + HNO3 + BrO + HOBr + BrNO2 + 2BrNO3 + MPN + ETHLN + MVKN + MCRHN + MCRHNB + PROPNN + R4N2 + PRN1 + PRPN + R4N1 + HONIT + MONITS + MONITU + OLND + OLNN + IHN1 + IHN2 + IHN3 + IHN4 + INPB + INPD + ICN + 2IDN + ITCN + ITHN + ISOPNOO1 + ISOPNOO2 + INO2B + INO2D + INA + IDHNBOO + IDHNDOO1 + IDHNDOO2 + IHPNBOO + IHPNDOO + ICNOO + 2IDNOO + MACRNO2 + ClO + HOCl + ClNO2 + 2ClNO3 + 2Cl2O2 + 2OClO + O + O1D + IO + HOI + IONO + 2IONO2 + 2OIO + 2I2O2 + 3I2O3 + 4I2O4;
LOx : O3 + NO2 + 2NO3 + PAN + PPN + MPAN + HNO4 + 3N2O5 + HNO3 + BrO + HOBr + BrNO2 + 2BrNO3 + MPN + ETHLN + MVKN + MCRHN + MCRHNB + PROPNN + R4N2 + PRN1 + PRPN + R4N1 + HONIT + MONITS + MONITU + OLND + OLNN + IHN1 + IHN2 + IHN3 + IHN4 + INPB + INPD + ICN + 2IDN + ITCN + ITHN + ISOPNOO1 + ISOPNOO2 + INO2B + INO2D + INA + IDHNBOO + IDHNDOO1 + IDHNDOO2 + IHPNBOO + IHPNDOO + ICNOO + 2IDNOO + MACRNO2 + ClO + HOCl + ClNO2 + 2ClNO3 + 2Cl2O2 + 2OClO + O + O1D + IO + HOI + IONO + 2IONO2 + 2OIO + 2I2O2 + 3I2O3 + 4I2O4;
PCO : CO;
LCO : CO;
PSO4 : SO4;
LCH4 : CH4;
PH2O2 : H2O2;


Note

The $$PO_x$$, $$LO_x$$, $$PCO$$, and $$LCO$$ families are used for computing budgets in the GEOS-Chem benchmark simulations. $$PSO4$$ is required for simulations using TOMAS aerosol microphysics.

To add a new prod/loss family, add a new line to the #FAMILIES section with the format

FAM_NAME : MEMBER_1 + MEMBER_2 + ... + MEMBER_N;


The family name must start with P or L to indicate whether KPP should calculate a production or a loss rate.

The maximum number of families allowed by KPP is currently set to 300. Depending on how many prod/loss families you add, you may need to increase that to a larger number to avoid errors in KPP. You can change the number for MAX_FAMILIES in KPP/kpp-code/src/gdata.h and then rebuild KPP.

// - Many limits can be changed here by adjusting the MAX_* constants
// - To increase the max size of inlined code (F90_GLOBAL etc.),
//   change MAX_INLINE in scan.h.
//
//   NOTES:
//   ------
//   (1) Note: MAX_EQN or MAX_SPECIES over 1023 causes a seg fault in CI build
//
//   (2) MacOS has a hard limit of 65332 bytes for stack memory.  To make
//       sure that you are using this max amount of stack memory, add
//       "ulimit -s 65532" in your .bashrc or .bash_aliases script.  We must
//       also set smaller limits for MAX_EQN and MAX_SPECIES here so that we
//       do not exceed the avaialble stack memory (which will result in the
//       infamous "Segmentation fault 11" error).  If you are stll having
//       problems on MacOS then consider reducing MAX_EQN and MAX_SPECIES
//       to smaller values than are listed below.
//         -- Bob Yantosca (03 May 2022)
#ifdef MACOS
#define MAX_EQN        2000     // Max number of equations (MacOS only)
#define MAX_SPECIES    1000     // Max number of species   (MacOS only)
#else
#define MAX_EQN       11000     // Max number of equations
#define MAX_SPECIES    6000     // Max number of species
#endif
#define MAX_SPNAME       30     // Max char length of species name
#define MAX_IVAL         40     // Max char length of species ID ?
#define MAX_EQNTAG       32     // Max length of equation ID in eqn file
#define MAX_K          1000     // Max length of rate expression in eqn file
#define MAX_ATOMS        10     // Max number of atoms
#define MAX_ATNAME       10     // Max char length of atom name
#define MAX_ATNR        250     // Max number of atom tables
#define MAX_PATH        300     // Max char length of directory paths
#define MAX_FILES        20     // Max number of files to open
#define MAX_FAMILIES    300     // Max number of family definitions
#define MAX_MEMBERS     150     // Max number of family members
#define MAX_EQNLEN      300     // Max char length of equations
#define MAX_EQNLEN      200


Important

When adding a prod/loss family or changing any of the other settings in gckpp.kpp, you must re-run KPP to produce new Fortran90 files for GEOS-Chem.

Production and loss families are archived via the HISTORY diagnostics. For more information, please see the Guide to GEOS_Chem History diagnostics on the GEOS-Chem wiki.

### Changing the numerical integrator¶

Several global options for KPP are listed at the top of the gckpp.kpp file:

#MINVERSION   2.5.0
#INTEGRATOR   rosenbrock
#LANGUAGE     Fortran90
#UPPERCASEF90 on
#DRIVER       none
#HESSIAN      off
#MEX          off
#STOICMAT     off
`

The #INTEGRATOR tag specifies the choice of numerical integrator that you wish to use with your chemical mechanism. The Rosenbrock solver is used by default for the GEOS-Chem fullchem and Hg mechanisms. But if you wish to use a different integrator for research purposes, you may select from several more options.

The #LANGUAGE should be set to Fortran90 and #UPPERCASEF90 should be set to on.

The #MINVERSION should be set to 2.5.0. This is the minimum KPP version you should be using with GEOS-Chem.

The other options should be left as they are, as they are not relevant to GEOS-Chem.