def convert(input_file, gen_dir, mech_dir, mcm_dir):
"""
This is the main function of this file. It takes as input an MCM file, and from it generates
5 files for use by AtChem2's Fortran code:
- 'Generic Rate Coefficients' and 'Complex reactions' go to gen_dir/mechanism.f90 with little more than formatting
changes - each line is replicated in full but with each named rate converted to an element in the vector q.
- The rates defined in 'Reaction definitions' also go to gen_dir/mechanism.f90 as elements of the vector p.
- The species involved as reactants (respectively products) in reactions in 'Reaction definitions' are split up into individual
species, and their species and reactions numbers go to mechanism.reac (respectively mechanism.prod). Combining
mechanism.reac, mechanism.prod and the last section of gen_dir/mechanism.f90 gives the original information
contained in 'Reaction definitions' but in the format that AtChem2 can parse.
- The numbers and names of all species encountered go to mechanism.species.
- The numbers and names of all RO2 species in 'Peroxy radicals' end up in mechanism.ro2.
:param input_file: string containing a relative or absolute reference to the mcm file to be processed.
:param gen_dir: string containing a relative or absolute reference to the directory in which the function should
place mechanism.f90. This is normally model/configuration.
:param mech_dir: string containing a relative or absolute reference to the directory in which the function should
place mechanism.{prod,reac,ro2,species}. This is normally model/configuration/ for the given model.
:param mcm_dir: string containing a relative or absolute reference to the directory housing the reference file peroxy-radicals_v3.3.1.
This is normally mcm/
"""
# Work out the values of directory and filename of input_file, and check their existence.
input_directory = os.path.dirname(os.path.abspath(input_file))
input_filename = os.path.basename(input_file)
assert os.path.isfile(os.path.join(input_directory, input_filename)), 'The input file ' + str(
os.path.join(input_directory, input_filename)) + ' does not exist.'
print input_directory
# Fix the input contents of any errant newlines
fix_mechanism_fac.fix_fac_full_file(os.path.join(input_directory, input_filename))
# Read in the input file
print 'Reading input file'
with open(os.path.join(input_directory, input_filename), 'r') as input_file:
s = input_file.readlines()
# split the lines into the following sections:
# - Ignore everything up to Generic Rate Coefficients
# - Generic Rate Coefficients
# - Complex reactions
# - Peroxy radicals
# - Reaction definitions
section_headers_indices = [0, 1, 2, 3]
section_headers = ['Generic Rate Coefficients', 'Complex reactions', 'Peroxy radicals', 'Reaction definitions']
generic_rate_coefficients = []
complex_reactions = []
peroxy_radicals = []
reaction_definitions = []
section = 0
for line in s:
for header_index in section_headers_indices:
if section_headers[header_index] in line:
section += 1
if section == 1:
generic_rate_coefficients.append(line)
elif section == 2:
complex_reactions.append(line)
elif section == 3:
peroxy_radicals.append(line)
elif section == 4:
reaction_definitions.append(line)
else:
assert section == 0, "Error, section is not in [0,4]"
# Convert peroxy_radicals to a list of strings, each of the RO2 species from 'Peroxy radicals'
ro2List = []
for item in peroxy_radicals:
if not re.match('\*', item):
# We have an equals sign on the first line. Handle this by splitting against =, then taking the last element of the
# resulting list, which will either be the right-hand side of the first line, or the whole of any other line.
# Similarly, the final line will end with a colon. Handle in a similar way.
# Then split by +. Append each item to ro2_input: multiple appends use 'extend'
ro2List.extend([elem.strip() for elem in item.split('=')[-1].split(';')[0].strip().split('+')])
# Remove empty strings
ro2List = filter(None, ro2List)
# Read in the reference RO2 species from the peroxy-radicals_v3.3.1 file
with open(os.path.join(mcm_dir, 'peroxy-radicals_v3.3.1'), 'r') as RO2List_file:
RO2List_reference = [r.rstrip() for r in RO2List_file.readlines()]
# Check each of the RO2s from 'Peroxy radicals' are in the reference RO2 list. If not print a warning at the top of
# mechanism.f90 for each errant species.
# TODO: This will break the exected format when mechanism.f90 is replaced by a parsable format.
print 'looping over inputted ro2s'
with open(os.path.join(gen_dir, 'mechanism.f90'), 'w') as mech_rates_file:
mech_rates_file.write("""! Note that this file is generated by tools/mech_converter.py
! based upon the file tools/mcm_example.fac
! Any manual edits to this file will be overwritten when
! calling tools/mech_converter.py
""")
for ro2_species in [element for element in ro2List if element not in RO2List_reference]:
print ' ****** Warning: ' + ro2_species + ' NOT found in RO2List ****** '
mech_rates_file.write('! ' + ro2_species +
' is not in the MCM list of RO2 species. Should it be in the RO2 sum?\n')
# Initialise list, dictionary and a counter.
mechanism_rates_coeff_list = []
variablesDict = dict()
reactionNumber = 0
# Process sections 1 and 2
# - copy comment lines across
# - other lines are reformatted to be Fortran syntax, then its contents edited to convert individual
# rate names to elements in a vector q.
for line in generic_rate_coefficients + complex_reactions:
# Check for comments (beginning with a !), or blank lines
if (re.match('!', line) is not None) or (line.isspace()):
mechanism_rates_coeff_list.append(line)
# Check for lines starting with either ; or *, and write these as comments
elif (re.match(';', line) is not None) or (re.match('[*]', line) is not None):
mechanism_rates_coeff_list.append('!' + line)
# Otherwise assume all remaining lines are in the correct format, and so process them
else:
# reactionNumber keeps track of the line we are processing
reactionNumber += 1
# This matches anything like @-dd.d and replaces with **(-dd.d). This uses (?<=@) as a lookbehind assertion,
# then matches - and any combination of digits and decimal points. This replaces the negative number by its
# bracketed version.
# It also then converts all @ to ** etc.
line2 = re.sub('(?<=@)-[0-9.]*',
'(\g<0>)',
line.replace(';', '').strip()
).replace('@', '**')
# Append _DP to the end of all digits that aren't followed by more digits or letters (targets a few too many)
line2 = re.sub('[0-9]+(?![a-zA-Z0-9\.])',
'\g<0>_DP',
line2)
# Undo the suffix _DP for any species names and for LOG10
line2 = re.sub(r'\b(?P<speciesnames>[a-zA-Z][a-zA-Z0-9]*)_DP',
'\g<speciesnames>',
line2)
# Undo the suffix _DP for any numbers like 1D7 or 2.3D-8
line2 = re.sub(r'\b(?P<doubles1>[0-9][0-9\.]*)[dDeE](?P<doubles2>[+-]*[0-9]+)_DP',
'\g<doubles1>e\g<doubles2>_DP',
line2)
# Add .0 to any literals that don't have a decimal place - this is necessary as it seems you can't use extended
# precision on such a number - gfortran complains about an unknown integer kind, when it should really be a real kind
line2 = re.sub(r'(?<![\.0-9+-dDeE])(?P<doubles>[0-9]+)_DP',
'\g<doubles>.0_DP',
line2)
# strip whitespace, ; and %
cleaned_line = line2.strip().strip('%;').strip()
# Process the assignment: split by = into variable names and values
[lhs, rhs] = re.split('=', cleaned_line)
# Strip each.
variable_name = lhs.strip()
value = rhs.strip()
# TODO: check for duplicates
variablesDict[variable_name] = reactionNumber
# Replace any variables declared here with references to q, with each new variable assigned
# to a new element of q.
new_rhs = tokenise_and_process(value, variablesDict)
# Save the resulting string to mechanism_rates_coeff_list
mechanism_rates_coeff_list.append('q('+str(variablesDict[variable_name]) + ') = ' + new_rhs + ' !' + cleaned_line + '\n')
# Save the number of such equations to be output to mechanism.{prod,reac}
numberOfGenericComplex = reactionNumber
# Initialise a few variables
speciesList = []
rateConstants = []
reactionNumber = 0
# Process 'Reaction definitions'. We process this before 'Peroxy radicals' because that relies on our
# SpeciesList generated here.
# - copy comment lines across
# - other lines are split into their consituent parts:
# - rateConstants are the reaction rates - these are processed via reformatting and tokenisation to use the vector q where needed.
# - the reactants and products of each species are collected up, numbered as necessary, and their placements output to mechanism.{prod,reac,species}
mech_reac_list = []
mech_prod_list = []
# Loop over all lines in the reaction_definitions section of the input file
for line in reaction_definitions:
# Check for comments (beginning with a !), or blank lines
if (re.match('!', line) is not None) or (line.isspace()):
rateConstants.append(line)
# Check for lines starting with either ; or *, and write these as comments
elif (re.match(';', line) is not None) or (re.match('[*]', line) is not None):
rateConstants.append('!' + line)
# Otherwise assume all remaining lines are in the correct format, and so process them
else:
# reactionNumber keeps track of the line we are processing
reactionNumber += 1
# strip whitespace, ; and %
line = line.strip().strip('%;').strip()
# split by the semi-colon : lhs is reaction rate, rhs is reaction equation
[lhs, rhs] = re.split(':', line)
# Add reaction rate to rateConstants
rateConstants.append(lhs)
# Process the reaction: split by = into reactants and products
[reactantsList, productsList] = re.split('=', rhs)
# Process each of reactants and products by splitting by +. Strip each at this stage.
reactants = [item.strip() for item in re.split('[+]', reactantsList)]
products = [item.strip() for item in re.split('[+]', productsList)]
# Ignore empty reactantsList
if not reactantsList == '':
# Compare each reactant against known species.
reactantNums = []
for x in reactants:
# If the reactant is a known species then add its number to reactantNums
if x in speciesList:
reactantNums.append(speciesList.index(x)+1)
else:
# Reactant x is not a known species.
# Add reactant to speciesList, and add this number to
# reactantNums to record this reaction.
speciesList.append(x)
reactantNums.append(len(speciesList))
# Write the reactants to mech_reac_list
mech_reac_list.extend([str(reactionNumber) + ' ' + str(z) + '\n' for z in reactantNums])
if not productsList == '':
# Compare each product against known species.
productNums = []
for x in products:
# If the reactant is a known species then add its number to reactantNums
if x in speciesList:
productNums.append(speciesList.index(x)+1)
else:
# Product x is not a known species.
# Add product to speciesList, add this number to
# productNums to record this reaction.
speciesList.append(x)
productNums.append(len(speciesList))
# Write the products to mechanism.prod
mech_prod_list.extend([str(reactionNumber) + ' ' + str(z) + '\n' for z in productNums])
with open(os.path.join(mech_dir, 'mechanism.prod'), 'w') as prod_file:
# Output number of species and number of reactions
prod_file.write(str(len(speciesList)) + ' ' + str(reactionNumber) + ' ' + str(numberOfGenericComplex) + ' numberOfSpecies numberOfReactions numberOfGenericComplex\n')
# Write all other lines
for line in mech_prod_list:
prod_file.write(line)
with open(os.path.join(mech_dir, 'mechanism.reac'), 'w') as reac_file:
# Output number of species and number of reactions
reac_file.write(str(len(speciesList)) + ' ' + str(reactionNumber) + ' ' + str(numberOfGenericComplex) + ' numberOfSpecies numberOfReactions numberOfGenericComplex\n')
# Write all other lines
for line in mech_reac_list:
reac_file.write(line)
# Write speciesList to mechanism.species, indexed by (1 to len(speciesList))
with open(os.path.join(mech_dir, 'mechanism.species'), 'w') as species_file:
for i, x in zip(range(1, len(speciesList) + 1), speciesList):
species_file.write(str(i) + ' ' + str(x) + '\n')
# Write out rate coefficients
i = 0
mech_rates_list = []
for rate_counter, x in zip(range(len(s)), rateConstants):
if (re.match('!', x) is not None) | (x.isspace()):
mech_rates_list.append(str(x))
else:
# This matches anything like @-dd.d and replaces with **(-dd.d). This uses (?<=@) as a lookbehind assertion,
# then matches - and any combination of digits and decimal points. This replaces the negative number by its
# bracketed version.
i += 1
string = re.sub('(?<=@)-[0-9.]*', '(\g<0>)', x)
# Now convert all @ to ** etc.
string = string.replace('@', '**')
string = string.replace('<', '(')
string = string.replace('>', ')')
# Replace any float-type numbers (xxx.xxxE+xx) with double-type - (xxx.xxxD+xx)
string = re.sub(r'(?P<single>[0-9]+\.[0-9]+)[eE]',
'\g<single>D',
string)
mech_rates_list.append('p(' + str(i) + ') = ' + \
tokenise_and_process(string, variablesDict) + ' !' + reaction_definitions[rate_counter])
# # Combine mechanism rates and RO2 sum files
with open(os.path.join(gen_dir, 'mechanism.f90'), 'a') as mech_rates_coeff_file:
mech_rates_coeff_file.write("""
module mechanism_mod
use, intrinsic :: iso_c_binding
contains
subroutine update_p(p, q, TEMP, N2, O2, M, RH, H2O, DEC, BLHEIGHT, DILUTE, JFAC, ROOFOPEN, J, RO2) bind(c,name='update_p')
implicit none
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, DEC, BLHEIGHT, DILUTE, JFAC, ROOFOPEN, J(:), RO2
""")
# Write out Generic Rate Coefficients and Complex reactions
for item in mechanism_rates_coeff_list:
mech_rates_coeff_file.write(item)
# Write out Reaction definitions
for r in mech_rates_list:
mech_rates_coeff_file.write(r)
mech_rates_coeff_file.write("""
end subroutine update_p
end module mechanism_mod
""")
# Finally, now that we have the full species list, we can output the RO2s to mechanism.ro2
# loop over RO2 and write the necessary line to mechanism.ro2, using the species number of the RO2
print 'adding RO2 to model/configuration/mechanism.ro2'
with open(os.path.join(mech_dir, 'mechanism.ro2'), 'w') as ro2_file:
ro2_file.write("""! Note that this file is generated by tools/mech_converter.py based upon the file tools/mcm_example.fac. Any manual edits to this file will be overwritten when calling tools/mech_converter.py
""")
for ro2List_i in ro2List:
for speciesNumber, y in zip(range(1, len(speciesList) + 1), speciesList):
if ro2List_i.strip() == y.strip():
ro2_file.write(str(speciesNumber) + ' !' + ro2List_i.strip() + '\n')
# Exit loop early if species found
break
# This code only executes if the break is NOT called, i.e. if the loop runs to completion without the RO2 being
# found in the species list
else:
ro2_file.write('0 ! error RO2 not in mechanism: ' + ro2List_i + '\n')
def convert(input_file):
script_directory = os.path.dirname(os.path.abspath(__file__))
input_directory = os.path.dirname(os.path.abspath(input_file))
input_filename = os.path.basename(input_file)
assert os.path.isfile(os.path.join(
input_directory, input_filename)), 'The input file ' + str(
os.path.join(input_directory, input_filename)) + ' does not exist.'
print input_directory
# Fix the input contents of any errant newlines
fix_mechanism_fac.fix_fac_full_file(
os.path.join(input_directory, input_filename))
# Read in the input file
print 'Reading input file'
with open(os.path.join(input_directory, input_filename),
'r') as input_file:
s = input_file.readlines()
# print s
# split the lines into the following sections:
# - Ignore everything up to Generic Rate Coefficients
# - Generic Rate Coefficients
# - Complex reactions
# - Peroxy radicals
# - Reaction definitions
section_headers_indices = [0, 1, 2, 3]
section_headers = [
'Generic Rate Coefficients', 'Complex reactions', 'Peroxy radicals',
'Reaction definitions'
]
generic_rate_coefficients = []
complex_reactions = []
peroxy_radicals = []
reaction_definitions = []
section = 0
for line in s:
for header_index in section_headers_indices:
if section_headers[header_index] in line:
section += 1
if section == 1:
# print line
generic_rate_coefficients.append(line)
elif section == 2:
# print line
complex_reactions.append(line)
elif section == 3:
# print line
peroxy_radicals.append(line)
elif section == 4:
# print line
reaction_definitions.append(line)
else:
assert section == 0, "Error, section is not in [0,4]"
# print line
# print 'generic_rate_coefficients'
# print generic_rate_coefficients
# print 'complex_reactions'
# print complex_reactions
# print 'peroxy_radicals'
# print peroxy_radicals
# print 'reaction_definitions'
# print reaction_definitions
# Initialise a few variables
speciesList = []
rateConstants = []
reactionNumber = 0
with open(os.path.join(input_directory, 'mechanism.reactemp'),
'w') as reac_temp_file, open(
os.path.join(input_directory, 'mechanism.prod'),
'w') as prod_file:
# Loop over all lines in the reaction_definitions section of the input file
for line in reaction_definitions:
# Check for comments (beginning with a !), or blank lines
if (re.match('!', line) is not None) | (line.isspace()):
rateConstants.append(line)
# Check for lines starting with either ; or *, and write these as comments
elif (re.match(';', line) is not None) | (re.match('[*]', line)
is not None):
rateConstants.append('!' + line)
# Otherwise assume all remaining lines are in the correct format, and so process them
else:
# reactionNumber keeps track of the line we are processing
reactionNumber += 1
# print 'line =', line
# strip whitespace, ; and %
line = line.strip().strip('%').strip(';').strip()
print ''
print 'line =', line
# split by the semi-colon : a[0] is reaction rate, a[1] is reaction equation
a = re.split(':', line)
# print 'a = ', a
# Add reaction rate to rateConstants
rateConstants.append(a[0])
# print 'rate =', a[0]
# Process the reaction: split by = into reactants and products
# print 'reaction = ', a[1]
reaction_parts = re.split('=', a[1])
# print reaction_parts
reactantsList = reaction_parts[0]
productsList = reaction_parts[1]
# print 'reactantlist = ', reactantsList
# print 'productlist = ', productsList
# Process each of reactants and products by splitting by +. Strip each at this stage.
reactants = [
item.strip() for item in re.split('[+]', reactantsList)
]
products = [
item.strip() for item in re.split('[+]', productsList)
]
# print 'reactants =', reactants
# print 'products =', products
# Ignore empty reactantsList
if not reactantsList == '':
# Compare each reactant against known species.
reactantNums = []
for x in reactants:
j = 0
for y in speciesList:
# Check for equality: if equality, then the reactant is a known species and its number should be
# added to the reactantNums variable
if x == y:
reactantNums.append(j + 1)
# print 'found:', y + ', j =', j
break
j += 1
# This code only executes if the break is NOT called, i.e. if the loop runs to completion without
# the reactant being found in the known species
else:
# Add reactant to speciesList, and add this number to
# reactantNums to record this reaction.
speciesList.append(x)
reactantNums.append(len(speciesList))
print 'adding', x, 'to speciesList'
# Write the reactants to mechanism.reactemp
for z in reactantNums:
reac_temp_file.write(
str(reactionNumber) + ' ' + str(z) + '\n')
if not productsList == '':
# Compare each product against known species.
productNums = []
for x in products:
j = 0
for y in speciesList:
# Check for equality: if equality, then the product is a known species and its number should be
# added to the productNums variable
if x == y:
productNums.append(j + 1)
# print 'found:', y + ', j =', j
break
j += 1
# This code only executes if the break is NOT called, i.e. if the loop runs to completion without
# the product being found in the known species
else:
# Add product to speciesList, add this number to
# productNums to record this reaction.
speciesList.append(x)
productNums.append(len(speciesList))
print 'adding', x, 'to speciesList'
# Write the products to mechanism.prod
for z in productNums:
prod_file.write(
str(reactionNumber) + ' ' + str(z) + '\n')
# Mark end of file with zeros
reac_temp_file.write('0\t0\t0\t0 \n')
prod_file.write('0\t0\t0\t0')
# Output number of species and number of reactions
reac_temp_file.write(
str(len(speciesList)) + ' ' + str(reactionNumber) +
' numberOfSpecies numberOfReactions\n')
# Copy mechanism.reactemp to mechanism.reac in a different order to make it readable by the model (move the last line to
# the first line).
with open(os.path.join(input_directory,
'mechanism.reactemp')) as reac_temp_file, open(
os.path.join(input_directory, 'mechanism.reac'),
'w') as reac_file:
st = reac_temp_file.readlines()
# Write last line
reac_file.write(st[len(st) - 1])
# Write all other lines
for line in st[:-1]:
reac_file.write(line)
# Write speciesList to mechanism.species, indexed by (1 to len(speciesList))
with open(os.path.join(input_directory, 'mechanism.species'),
'w') as species_file:
for i, x in zip(range(1, len(speciesList) + 1), speciesList):
species_file.write(str(i) + ' ' + str(x) + '\n')
# Write out rate coefficients
i = 1
with open(
os.path.join(input_directory, 'mechanism-rate-coefficients.ftemp'),
'w') as mech_rates_temp_file:
for rate_counter, x in zip(range(len(s)), rateConstants):
if (re.match('!', x) is not None) | (x.isspace()):
mech_rates_temp_file.write(str(x))
else:
# This matches anything like @-dd.d and replaces with **(-dd.d). This uses (?<=@) as a lookbehind assertion,
# then matches - and any combination of digits and decimal points. This replaces the negative number by its
# bracketed version.
string = re.sub('(?<=@)-[0-9.]*', '(\g<0>)', x)
# Now convert all @ to ** etc.
string = string.replace('@', '**')
string = string.replace('<', '(')
string = string.replace('>', ')')
mech_rates_temp_file.write(' p(' + str(i) + ') = ' + string +
' !' +
reaction_definitions[rate_counter])
i += 1
# Write RO2 data to file
in_RO2_lines = False
ro2_input = []
for item in peroxy_radicals:
if not in_RO2_lines:
# Check to see whether we are entering the 'Reaction definitions' section
if 'RO2 = ' in item:
in_RO2_lines = True
if in_RO2_lines:
if not re.match('\*', item):
ro2_input.append(item)
else:
in_RO2_lines = False
ro2List = []
for l in ro2_input:
# We have an equals sign on the first line. Handle this by splitting against =, then taking the last element of the
# resulting list, which will either be the right-hand side of the first line, or the whole of any other line.
# Then split by +.
strArray = l.split('=')[-1].split('+')
# print strArray
# For each element, remove any semi-colons, strip, and then append if non-empty.
for x in strArray:
x = x.replace(';', '').strip()
if x == '':
pass
# print 'doing nothing'
else:
# print x
ro2List.append(x)
# check RO2s are in RO2 list
with open(os.path.join(script_directory, 'RO2listv3.3.1')) as RO2List_file:
RO2List_input = RO2List_file.readlines()
for r in RO2List_input:
r = r.strip()
# print r
# Check that each species is in the RO2 list. If so, just print to screen. Otherwise, print a warning at the top of
# mechanism-rate-coefficients.f90 for each errant species.
print 'looping over inputted ro2s'
# print 'The RO2List is: ', ro2List
with open(os.path.join(input_directory, 'mechanism-rate-coefficients.f90'),
'w') as mech_rates_file:
mech_rates_file.write(
"""! Note that this file is generated by tools/mech_converter.py,
! based upon the file tools/mcm_subset.fac. Any manual edits to this file will be overwritten
! when calling tools/mech_converter.py
""")
for ro2List_i in ro2List:
for ro2List_input_j in RO2List_input:
if ro2List_i.strip() == ro2List_input_j.strip():
# print ro2List_i.strip() + ' found in RO2List'
break
# This code only executes if the break is NOT called, i.e. if the loop runs to completion without the species
# being found in the RO2 list
else:
print ' ****** Warning: ' + ro2List_i.strip(
) + ' NOT found in RO2List ****** '
mech_rates_file.write(
'! ' + ro2List_i.strip() +
' is not in the MCM list of RO2 species. Should it be in the RO2 sum?\n'
)
# loop over RO2 and write the necessary line to mechanism-rate-coefficients.f90, using the species number of the RO2
mech_rates_file.write(' ro2 = 0.00e+00\n')
print 'adding RO2 to mechanism-rate-coefficients.f90'
for ro2List_i in ro2List:
# print 'ro2List_i: ' + ro2List_i
for speciesNumber, y in zip(range(1,
len(speciesList) + 1),
speciesList):
if ro2List_i.strip() == y.strip():
mech_rates_file.write(' ro2 = ro2 + y(' +
str(speciesNumber) + ')!' +
ro2List_i.strip() + '\n')
# Exit loop early if species found
break
# This code only executes if the break is NOT called, i.e. if the loop runs to completion without the RO2 being
# found in the species list
else:
mech_rates_file.write('\t ! error RO2 not in mechanism: ' +
ro2List_i + '\n')
mech_rates_file.write('\n\n')
# Read in NOY data, which is arrange as 'NOY = blah + blah + blah \n + blah + blah ;'
# with open('./NOY.fac') as NOY_fac_file
# NOY_input = NOY_fac_file.readlines()
#
# NOYList = []
# for n in NOY_input:
# # We have an equals sign on the first line. Handle this by splitting against =, then taking the last element of the
# # resulting list, which will either be the right-hand side of the first line, or the whole of any other line.
# # Then split by +
# strArray = n.split('=')[-1].split('+')
#
# print strArray
# # For each element, remove any semi-colons, strip, and then append if non-empty.
# for x in strArray:
# x = x.replace(';', '').strip()
# if x == '':
# print 'doing nothing'
# else:
# print x
# NOYList.append(x)
#
# # loop over NOY and write the necessary line to mechanism-rate-coefficients.f90, using the species number of the NOY
# mech_rates_file.write('\tNOY = 0.00e+00\n')
# for NOYList_i in NOYList:
# print 'NOYList_i: ' + NOYList_i
# for speciesNumber, y in zip(range(1, len(speciesList)+1), speciesList):
# if NOYList_i.strip() == y.strip():
# mech_rates_file.write(' NOY = NOY + y(' + str(speciesNumber) + ')!' + NOYList_i.strip() + '\n')
# # Exit loop early if species found
# break
# # This code only executes if the break is NOT called, i.e. if the loop runs to completion without the NOY being
# # found in the species list
# else:
# mech_rates_file.write('\t !error NOY not in mechanism: ' + NOYList_i + '\n')
#
# mech_rates_file.write('\n\n')
# # Combine mechanism rates and RO2 / NOY sum files
with open(
os.path.join(input_directory,
'mechanism-rate-coefficients.ftemp')
) as mech_rates_temp_file:
rs = mech_rates_temp_file.readlines()
for r in rs:
mech_rates_file.write(r)
os.remove(os.path.join(input_directory, 'mechanism.reactemp'))
os.remove(
os.path.join(input_directory, 'mechanism-rate-coefficients.ftemp'))
mechanism_rates_list = [
"""
! Note that this file is generated by tools/mech_converter.py,
! based upon the file tools/mcm_subset.fac. Any manual edits to this file will be overwritten
! when calling tools/mech_converter.py
SUBROUTINE mechanism_rates (p, t, y, mnsp)
USE photolysisRates
USE zenithData1
USE constraints
USE envVars, ONLY: ro2
IMPLICIT NONE
! calculates rate constants from arrhenius information
DOUBLE PRECISION, INTENT (out) :: p(*)
DOUBLE PRECISION, INTENT (in) :: t
INTEGER, INTENT (in) :: mnsp
DOUBLE PRECISION, INTENT (in) :: y(mnsp)
DOUBLE PRECISION :: temp, pressure, dummy
"""
]
mechanism_rates_list.append("""
! declare variables missed in MCM definition
INTEGER :: i
DOUBLE PRECISION :: photoRateAtT
INCLUDE 'modelConfiguration/mechanism-rate-declarations.f90'
CALL ro2sum (ro2, y)
dummy = y(1)
dec = -1e16
CALL getEnvVarsAtT (t, temp, rh, h2o, dec, pressure, m, blh, dilute, jfac, roofOpen)
CALL atmosphere (o2, n2, m)
!O2 = 0.2095*m
!N2 = 0.7809*m
! * **** SIMPLE RATE COEFFICIENTS ***** *""")
coeffSpeciesList = [
'N2', 'O2', 'M', 'RH', 'H2O', 'DEC', 'BLH', 'DILUTE', 'JFAC',
'ROOFOPEN'
]
reactionNumber = 0
# P
for line in generic_rate_coefficients + complex_reactions:
# Check for comments (beginning with a !), or blank lines
if (re.match('!', line) is not None) | (line.isspace()):
mechanism_rates_list.append(' ' + line)
# Check for lines starting with either ; or *, and write these as comments
elif (re.match(';', line) is not None) | (re.match('[*]', line)
is not None):
mechanism_rates_list.append(' !' + line)
# Otherwise assume all remaining lines are in the correct format, and so process them
else:
# This matches anything like @-dd.d and replaces with **(-dd.d). This uses (?<=@) as a lookbehind assertion,
# then matches - and any combination of digits and decimal points. This replaces the negative number by its
# bracketed version.
# It also then converts all @ to ** etc.
# Save the resulting string to mechanism_rates_list
mechanism_rates_list.append(
' ' +
re.sub('(?<=@)-[0-9.]*', '(\g<0>)',
line.replace(';', '').strip()).replace('@', '**') +
'\n')
# Now we need to find the list of all species that are used in these equations, so we can declare them
# at the top of the Fortran source file.
# reactionNumber keeps track of the line we are processing
reactionNumber += 1
# print 'line =', line
# strip whitespace, ; and %
line = line.strip().strip('%').strip(';').strip()
print 'line =', line
# split by the semi-colon : a[0] is reaction rate, a[1] is reaction equation
a = line
# print 'a = ', a
# Add reaction rate to rateConstants
# rateConstant = a[0]
# rateConstants.append(rateConstant)
# print rateConstant
# Process the reaction: split by = into reactants and products
# print 'reaction =', a
reaction_parts = re.split('=', a)
# print reaction_parts
LHSList = reaction_parts[0]
RHSList = reaction_parts[1]
# print 'reactantlist = ', LHSList
# print 'productlist = ', RHSList
# Process each of reactants and products by splitting by +. Strip each at this stage.
reactant = LHSList.strip(
) # [item.strip() for item in re.split('[+]', LHSList)]
products = RHSList.strip(
) # [item.strip() for item in re.split('[+]', RHSList)]
# print 'reactants = ', reactants
# print 'products = ', products
# Compare reactant against known species.
if reactant in coeffSpeciesList:
pass
# print 'found:', reactant
else:
# Add reactant to coeffSpeciesList, and add this number to
# reactantNums to record this reaction.
coeffSpeciesList.append(reactant)
print 'adding', reactant, 'to coeffSpeciesList'
if not RHSList.isspace():
# Compare each product against known species.
productNums = []
# print RHSList
# Replace all math characters and brackets with spaces, and split the remaining string by spaces.
# Now, each string in the sublist will:
# - start with a digit
# - be a 'reserved word' i.e. LOG10, EXP, TEMP, PRESSURE
# - otherwise, be a species
RHSList_sub = re.sub('[()\-+*@/]', ' ', RHSList).split(' ')
# print RHSList_sub
RHSList_sub = [item.upper() for item in RHSList_sub]
for x in RHSList_sub:
# Filter out spaces, numbers, and maths symbols
if (not re.match('[0-9]', x)) and (not x == ''):
# Filter out our 'reserved words'
if not any(x == reserved for reserved in
['EXP', 'TEMP', 'PRESSURE', 'LOG10', 'T']):
# print x
if x in coeffSpeciesList:
pass
# print 'found: ', x
else:
coeffSpeciesList.append(x)
print 'adding', x, 'to coeffSpeciesList'
# Recombine the species found into lines of 10 in the right format to declare them as Fortran variables.
# Begin wthe first line as necessary
newline = ' DOUBLE PRECISION ::'
mechanism_rates_decl = []
# Loop over all species
for i, item in zip(range(1, len(coeffSpeciesList) + 1), coeffSpeciesList):
# Add the next species
newline += ' ' + item.strip()
# If it's the last species, then exit the loop with some extra newlines
if i == len(coeffSpeciesList):
mechanism_rates_decl.append(newline + '\n\n\n')
continue
# Otherwise, every tenth species gets rounded off with a newline and a prefix to the next line
if i % 10 == 0:
mechanism_rates_decl.append(newline + '\n')
newline = ' DOUBLE PRECISION ::'
else:
# If not, add a spacer
newline += ','
# Insert the list generated above into the right place in the master list
mechanism_rates_list = list(
mechanism_rates_list[0]) + mechanism_rates_decl + list(
mechanism_rates_list[1:])
mechanism_rates_list.append(""" DO i = 1, nrOfPhotoRates
IF (useConstantValues==0) THEN
IF (cosx<1.00d-10) THEN
j(ck(i)) = 1.0d-30
ELSE
j(ck(i)) = cl(i)*cosx**(cmm(i))*EXP(-cnn(i)*secx)*transmissionFactor(i)*roofOpen*jfac
ENDIF
ELSE
j(ck(i)) = cl(i)
ENDIF
ENDDO
DO i = 1, numConPhotoRates
CALL getConstrainedQuantAtT2D (t, photoX, photoY, photoY2, photoNumberOfPoints(i), photoRateAtT, 2, i, &
maxNumberOfDataPoints, numConPhotoRates)
j(constrainedPhotoRatesNumbers(i)) = photoRateAtT
ENDDO
INCLUDE 'modelConfiguration/mechanism-rate-coefficients.f90'
RETURN
END SUBROUTINE mechanism_rates
INCLUDE 'modelConfiguration/extraOutputSubroutines.f90'
""")
# print mechanism_rates_list
with open(os.path.join(script_directory, '../mechanism-rates.f90'),
'w+') as mr2_file:
for item in mechanism_rates_list:
mr2_file.write(item)
