Merge pull request #507 from AlfredMayhew/custom_functions

Specifying Custom FORTRAN Functions in the Mechanism

build/mech_converter.py

@@ -24,7 +24,7 @@
 # - mechanism.ro2
 # - mechanism.f90
 #
-# Acknowledgements: B. Nelson, M. Newland
+# Acknowledgements: B. Nelson, M. Newland, A. Mayhew
 #
 # ARGUMENTS:
 # 1. path to the mechanism .fac file
@@ -71,9 +71,10 @@ def tokenise_and_process(input_string, vars_dict):
  assert isinstance(vars_dict, dict), \
  'tokenise_and_process: vars_dict is not of type dict: ' + str(vars_dict)
 
- # Generate start and end points of sections of symbols and non-symbols.
- symbol_regex = r'[()\-+*@/ ]+'
- nonsymbol_regex = r'[^()\-+*@/ ]+'
+ # Generate start and end points of sections of symbols and nonsymbols
+ symbol_regex = '[()\-+*@/, ]+'
+ nonsymbol_regex = '[^()\-+*@/, ]+'
+
  list_of_symbol_starts = [m.start(0) for m in re.finditer(symbol_regex, input_string)]
  list_of_symbol_ends = [m.end(0) for m in re.finditer(symbol_regex, input_string)]
  list_of_nonsymbol_starts = [m.start(0) for m in re.finditer(nonsymbol_regex, input_string)]
@@ -302,6 +303,15 @@ def convert_to_fortran(input_file, mech_dir, mcm_vers):
  continue
 
  # -------------------------------------------------
+ # Read in the names of user-defined custom rate functions and add them
+ # to the list of reserved names so that they will be carried through the 
+ # rate definitions (in a similar manner to LOG10)
+ with open(mech_dir + '/customRateFuncs.f90') as custom_func_file:
+ func_def_pat = "function +([a-zA-Z0-9_]*) *\("
+ custom_func_names = re.findall(func_def_pat, custom_func_file.read(), re.I)
+
+ for n in custom_func_names:
+ reservedOtherList.append(n)
 
  # Initialise list, dictionary and a counter.
  mechanism_rates_coeff_list = []
@@ -551,6 +561,7 @@ def convert_to_fortran(input_file, mech_dir, mcm_vers):
 
  subroutine update_p(p, q, TEMP, N2, O2, M, RH, H2O, BLHEIGHT, DEC, JFAC, DILUTE, ROOFOPEN, ASA, J, RO2) bind(c,name='update_p')
 
+ use custom_functions_mod
  integer, parameter :: DP = selected_real_kind( p = 15, r = 307 )
  real(c_double), intent(inout) :: p(*), q(*)
  real(c_double), intent(in) :: TEMP, N2, O2, M, RH, H2O, BLHEIGHT, DEC, JFAC, DILUTE, ROOFOPEN, ASA, J(*), RO2

model/configuration/.gitignore

@@ -1,2 +1,3 @@
 # Ignore auto-generated mechanism files in this directory
 mechanism.*
+customRateFuncs.o

model/configuration/customRateFuncs.f90

@@ -0,0 +1,29 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ !Define your functions here.
+
+end module custom_functions_mod

tests/.gitignore

@@ -9,6 +9,7 @@ mechanism.reac
 mechanism.ro2
 mechanism.species
 mechanism.so
+customRateFuncs.o
 tests/*/output/reactionRates/*
 model_tests/*/output/reactionRates/*
 

tests/model_tests/INFO.md

@@ -24,4 +24,6 @@ starting at 6:30 am on 9/11/2008.
 
 - `spec_model_kpp` is the same as the base case but the mechanism is in KPP format.
 
-- `spec_model_stoich` is the same as the base case but the mechanism has been adjusted to include stoichometric coefficients (e.g. 'NO + NO = NO2 + NO2' becomes '2 NO = 2 NO2')
+- `spec_model_stoich` is the same as the base case but the mechanism has been adjusted to include stoichometric coefficients (e.g. 'NO + NO = NO2 + NO2' becomes '2 NO = 2 NO2')
+
+- `spec_model_func` is the same as the base case but the KMT15 rate definition has been moved to `customRateFuncs.f90` as opposed to being defined in the mechanism.

tests/model_tests/env_model_1/configuration/customRateFuncs.f90

@@ -0,0 +1,29 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ !Define your functions here.
+
+end module custom_functions_mod

tests/model_tests/env_model_2/configuration/customRateFuncs.f90

@@ -0,0 +1,29 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ !Define your functions here.
+
+end module custom_functions_mod

tests/model_tests/env_model_3/configuration/customRateFuncs.f90

@@ -0,0 +1,29 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ !Define your functions here.
+
+end module custom_functions_mod

tests/model_tests/env_model_4/configuration/customRateFuncs.f90

@@ -0,0 +1,29 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ !Define your functions here.
+
+end module custom_functions_mod

tests/model_tests/firstorder/configuration/customRateFuncs.f90

@@ -0,0 +1,29 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ !Define your functions here.
+
+end module custom_functions_mod

tests/model_tests/secondorder/configuration/customRateFuncs.f90

@@ -0,0 +1,29 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ !Define your functions here.
+
+end module custom_functions_mod

tests/model_tests/spec_model_1/configuration/customRateFuncs.f90

@@ -0,0 +1,29 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ !Define your functions here.
+
+end module custom_functions_mod

tests/model_tests/spec_model_func/configuration/customRateFuncs.f90

@@ -0,0 +1,45 @@
+! -----------------------------------------------------------------------------
+!
+! Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
+! Peter Jimack, Mike Pilling
+!
+! Copyright (c) 2017 Sam Cox, Roberto Sommariva
+!
+! Copyright (c) 2023 Alfred Mayhew
+!
+! This file is part of the AtChem2 software package.
+!
+! This file is covered by the MIT license which can be found in the file
+! LICENSE.md at the top level of the AtChem2 distribution.
+!
+! -----------------------------------------------------------------------------
+! ******************************************************************** !
+! ATCHEM2 -- MODULE customRateFunctions
+!
+! This module contains user-defined functions that can be referenced
+! in the mechanism file
+! ******************************************************************** !
+module custom_functions_mod
+ implicit none
+
+contains
+
+ ! -----------------------------------------------------------------
+ ! Calculates the rate of KMT15
+ pure function calcKMT15( t, m ) result ( KMT15 )
+ real*8, intent(in) :: t, m
+ real :: K150, K15I, KR15, FC15, NC15, F15
+ real :: KMT15
+
+ K150 = 8.6E-29 * m * (t / 300)**(-3.1)
+ K15I = 9.0E-12 * (t / 300)**(-0.85)
+ KR15 = K150 / K15I
+ FC15 = 0.48
+ NC15 = 0.75 - 1.27 * (LOG10(FC15))
+ F15 = 10**(LOG10(FC15) / (1 + (LOG10(KR15) / NC15)**2))
+ KMT15 = (K150*K15I)*F15/(K150+K15I)
+
+ return
+ end function calcKMT15
+
+end module custom_functions_mod

tests/model_tests/spec_model_func/configuration/environmentVariables.config

@@ -0,0 +1,10 @@
+1 TEMP 291.45
+2 PRESS 950.2
+3 RH 67.4
+4 H2O CALC
+5 DEC CALC
+6 BLHEIGHT NOTUSED
+7 DILUTE NOTUSED
+8 JFAC NOTUSED
+9 ROOF OPEN
+10 ASA NOTUSED

tests/model_tests/spec_model_func/configuration/initialConcentrations.config

@@ -0,0 +1,5 @@
+CO 4.8e+12
+O3 6.11e11
+NO 6.8e10
+NO2 8.37e10
+C2H4 2.76e+9