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Specifying Custom FORTRAN Functions in the Mechanism #507

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Jan 17, 2024
Merged

Specifying Custom FORTRAN Functions in the Mechanism #507

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75ddc38
Added ability to specify custom fortran functions that can be called …
AlfredMayhew Oct 2, 2023
7525299
Ignoring commas in rate expressions as they might be separating funct…
AlfredMayhew Oct 3, 2023
17a3fb9
Copied custom rate function skeleton file into test configuration dir…
AlfredMayhew Dec 23, 2023
d2af359
Added a test for the custom functions file, replacing KMT15
AlfredMayhew Jan 3, 2024
6612b54
Updated test to use the correct .cmp files and allow the test to pass
AlfredMayhew Jan 4, 2024
53e209d
Added custom rate file for the new stoichiometry test from a recent u…
AlfredMayhew Jan 5, 2024
44e1a06
Added my name to acknowledgements
AlfredMayhew Jan 11, 2024
d4042c3
Added copyright headers to each of the customRateFuncs.f90 files
AlfredMayhew Jan 11, 2024
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19 changes: 15 additions & 4 deletions build/mech_converter.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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)]
Expand Down Expand Up @@ -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 = []
Expand Down Expand Up @@ -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
Expand Down
1 change: 1 addition & 0 deletions model/configuration/.gitignore
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@@ -1,2 +1,3 @@
# Ignore auto-generated mechanism files in this directory
mechanism.*
customRateFuncs.o
29 changes: 29 additions & 0 deletions model/configuration/customRateFuncs.f90
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@@ -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
1 change: 1 addition & 0 deletions tests/.gitignore
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Expand Up @@ -9,6 +9,7 @@ mechanism.reac
mechanism.ro2
mechanism.species
mechanism.so
customRateFuncs.o
tests/*/output/reactionRates/*
model_tests/*/output/reactionRates/*

Expand Down
4 changes: 3 additions & 1 deletion tests/model_tests/INFO.md
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Expand Up @@ -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.
29 changes: 29 additions & 0 deletions tests/model_tests/env_model_1/configuration/customRateFuncs.f90
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! -----------------------------------------------------------------------------
!
! 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
29 changes: 29 additions & 0 deletions tests/model_tests/env_model_2/configuration/customRateFuncs.f90
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! -----------------------------------------------------------------------------
!
! 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
29 changes: 29 additions & 0 deletions tests/model_tests/env_model_3/configuration/customRateFuncs.f90
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! -----------------------------------------------------------------------------
!
! 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
29 changes: 29 additions & 0 deletions tests/model_tests/env_model_4/configuration/customRateFuncs.f90
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! -----------------------------------------------------------------------------
!
! 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
29 changes: 29 additions & 0 deletions tests/model_tests/firstorder/configuration/customRateFuncs.f90
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! -----------------------------------------------------------------------------
!
! 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
29 changes: 29 additions & 0 deletions tests/model_tests/secondorder/configuration/customRateFuncs.f90
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! -----------------------------------------------------------------------------
!
! 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
29 changes: 29 additions & 0 deletions tests/model_tests/spec_model_1/configuration/customRateFuncs.f90
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! -----------------------------------------------------------------------------
!
! 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
45 changes: 45 additions & 0 deletions tests/model_tests/spec_model_func/configuration/customRateFuncs.f90
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! -----------------------------------------------------------------------------
!
! 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
10 changes: 10 additions & 0 deletions tests/model_tests/spec_model_func/configuration/environmentVariables.config
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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
5 changes: 5 additions & 0 deletions tests/model_tests/spec_model_func/configuration/initialConcentrations.config
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CO 4.8e+12
O3 6.11e11
NO 6.8e10
NO2 8.37e10
C2H4 2.76e+9
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