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https://github.com/barronh/pykpp

pykpp is a KPP-like chemical mechanism parser that produces a box model solvable by SciPy's odeint solver
https://github.com/barronh/pykpp

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pykpp is a KPP-like chemical mechanism parser that produces a box model solvable by SciPy's odeint solver

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README 

        
pykpp

=====



pykpp is a KPP-like chemical mechanism parser that produces a box model solvable by SciPy's odeint solver



Run Examples No installation

----------------------------

* Requires a google account.

* Uses Google's Colab

* Click Badge [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/barronh/pykpp/)



Running Instructions

--------------------



1. Open DOS Prompt on Windows or Terminal on Linux/Mac OSX

2. Type "python -m pykpp model.kpp" where model.kpp is a valid KPP input file.

3. Example below assumes Installation and that mcm_ch4.kpp has been downloaded to the working folder



```

$ python -m pykpp mcm_ch4.kpp --solver="odeint,rtol=1e-5,atol=[1e-5 if s != 'O1D' else 1 for s in out.allspcs]"

Found PYTHON!

Species: 30 

Reactions: 68

/Users/barronh/Development/pykpp/src/pykpp/updaters.py:7: UserWarning: Using RO2 = 1e-32 @ 18000.0

  def __init__(self, *args, **kwds):

 0.0%: {t:18000,O3:60,NO2:4.1E-43,RO2/CFACTOR:4.1E-43}

 1.0%: {t:18301,O3:59,NO2:0.98,RO2/CFACTOR:4.1E-43}

 2.1%: {t:18606,O3:59,NO2:0.98,RO2/CFACTOR:7.7E-05}

...

98.8%: {t:46464,O3:58,NO2:0.041,RO2/CFACTOR:0.046}

100.1%: {t:46837,O3:57,NO2:0.039,RO2/CFACTOR:0.047}

Solved in 0.410105 seconds

```



* Example input files can be downloaded from https://github.com/barronh/pykpp/tree/master/src/pykpp/models and are also in the models folder of pykpp source



Install Instructions

--------------------



Instructions

------------



1. Install Anaconda (https://www.continuum.io/downloads)

2. Download release version zip file from github. (or source)

3. Extract zip file

4. navigate to extracted folder pykpp-X.Y (the unzipped folder from pykpp-X.Y.zip)

5. Install pykpp from DOS terminal or terminal on Mac/Linux



    DOS: `python.exe setup.py install`

    Terminal: `python setup.py install`



6. Run `simple_organic` test case

  1. Copy `simple_organic.kpp` and `ekma.py` from test folder (either through github or from source

  2. navigate to where you downloaded `simple_organic.kpp` and `ekma.py`

7. Run pykpp



    DOS: `python.exe -m pykpp simple_organic.kpp -c ekma.py`

    Terminal: `python -m pykpp simple_organic.kpp -c ekma.py`



8. Compare ekma.png, which is an EKMA diagram, to `Figure 6.12 from Seinfeld & Pandis ACP 2nd ed. 2006` (search Google Books for that phrase to compare).

9. Do something more complicated (see Using pykpp with MCM)



Using pykpp with a MCM Extraction

---------------------------------



Adapt mcm kpp output for pykpp following these steps.



1. Fix line endings (mixed linux/windows)

2. Remove header comment (First 16 lines)

3. Remove everything above `#INCLUDE F90_RCONST`

4. replace `F90_RCONST` with `PY_UTIL`

5. replace `USE constants` with 2 lines



    `add_world_updater(func_updater(Update_M, incr = 300))`

    `add_world_updater(func_updater(Update_THETA, incr = 300))`

    

6. remove comment lines (preceded by `!`)

7. replace `RO2 = & C(ind_XXX1) + C(ind_XXX2) + ....` with `RO2 = y[[ind_XXX1, ind_XXX2, ...]].sum()`

8. remove `CALL mcm_constants(time, temp, M, N2, O2, RO2, H2O) ` line

9. replace all `D-` and `D+` wit `e-` and `e+` (also check for `#D#`, which is an implicit +, and replace as necessary)

10. wrap code in `add_world_updater(code_updater("""""", incr = 300))`



For example, methane chemistry changes from 



```

{********************************************************************* ;

* A citation to the MCM website and the relevant mechanism          * ;

* construction protocols should be given in any publication using   * ;

* information obtained from this source, using the following or     * ;

* comparable wording:                                               * ;

* The chemical mechanistic information was taken from the Master    * ;

* Chemical Mechanism, MCM v3.3.1 (ref), via website:                  * ;

* http://mcm.leeds.ac.uk/MCM.                                       * ;

* The reference should be: (Jenkin et al., Atmos. Environ., 31, 81, * ;

* 1997; Saunders et al., Atmos. Chem. Phys., 3, 161, 2003), for     * ;

* non aromatic schemes; (Jenkin et al., Atmos. Chem. Phys., 3,  * ;

* 181, 2003; Bloss et al., Atmos. Chem. Phys., 5, 641, 2005), for   * ;

* aromatic schemes; (Jenkin et al., Atmos. Chem. Phys.,  12, * ;

* 5275, 2012), for the beta-caryophyllene scheme and (Jenkin et al., ;

* Atmos. Chem. Phys., 15, 11433, 2015), for the isoprene scheme.    * ;

********************************************************************* ;}

#INLINE F90_GLOBAL 

 REAL(dp)::M, N2, O2, RO2, H2O 

 #ENDINLINE {above lines go into MODULE KPP_ROOT_Global}

#INCLUDE atoms 

#DEFVAR

HCHO = IGNORE ;

...

#INLINE F90_RCONST

 USE constants

 !end of USE statements 

 !

 ! start of executable statements

 RO2 = & 

 C(ind_CH3O2) 

 KRO2NO = 2.7D-12*EXP(360/TEMP)

KRO2HO2 = 2.91D-13*EXP(1300/TEMP)

...

#ENDINLINE

```



and become



```

#INLINE PY_UTIL

add_world_updater(func_updater(Update_M, incr = 300))

add_world_updater(func_updater(Update_THETA, incr = 300))

add_world_updater(code_updater("""

EXP = exp

LOG10 = log10

try:

    RO2 = y[[ind_CH3O2]].sum()

except:

    warn('Using RO2 = 1e-32 @ %s' % t)

    RO2 = 1e-32



KRO2NO = 2.7e-12*EXP(360/TEMP)

KRO2HO2 = 2.91e-13*EXP(1300/TEMP)

KBPPN = (KPPN0*KPPNI)*FCPPN/(KPPN0+KPPNI)

""", incr = 300, message = 'MCM')

```



11. Replace `= :` with `= DUMMY :` in equations

12. Replace `J(##)` with `MCMJ(##, THETA)`

13. Move any species you want as constants from reactants to rate constant and comment them out as products.

14. Add intialization code. For example,



```

#INLINE PY_INIT

DT = 300

TSTART = 5 * 3600.

TEND = TSTART + 8 * 3600

P = 101325.

TEMP = 298.

H2O = h2o_from_rh_and_temp(80., TEMP)

StartDate = 'datetime(2013, 6, 1)'

Latitude_Degrees = 35.

Longitude_Degrees = 0.00E+00

#ENDINLINE



#INITVALUES

CFACTOR = P * Avogadro / R / TEMP * centi **3 * nano {ppb-to-molecules/cm3}

ALL_SPEC=1e-32;

CH4 = 1850

NO = 1.

NO2 = 7.

O3 = 60.

```



The mcm_ch4.kpp file under pykpp/models was extracted by selecting CH4 from the MCM website, and exporting KPP format with inorganic reactions and rate constants on 2016-01-28 at 10:00am and converted following the steps described above. It can be used as a reference.