def read_globchem_dat(filename):
"""
Read and parse the "globchem.dat" globchem_file (SMVGEARII syntax).
Parameters
----------
filename : string
Filename or path to the global chemistry globchem_file (globchem.dat)
Returns
-------
header : string
header (commented text) of the file
mb_groups : dict
mass balance groups (id, status): used for mass balance capability of
chemical solvers (SMVGEARII or KPP)
species : dict
chemical species
reac_kn : dict
list of chemical kinectic reactions
reac_ph : dict
list of photolysis reactions
species_links : list of tuples
links between species made by the kinectic reactions
"""
species = dict()
reac_kn = dict()
reac_ph = dict()
species_links = list()
# keys of 'species' and 'reac' dictionnaries
species_keys = [
'ord_n', 'fline', 'status', 'id', 'absorption', 'atomic_mass',
'init_concentration', 'mb_groups', 'formula', 'name'
]
reac_keys = [
'ord_n', 'fline', 'status', 'flag', 'comment', 'rate', 'reactants',
'products', 'coefs'
]
def sanatize_str_inlist(l):
"""
clean (strip...) string items in a list
"""
return ([x.strip() if type(x) is str else x for x in l])
def go_2_begin(globchem_file, fline):
"""
jump lines in the text file until reading the line
with the word "BEGIN"
"""
jumptext = ""
while True:
text = globchem_file.readline().strip()
fline += 1
if (text == "BEGIN"):
break
else:
jumptext += text + '\n'
return jumptext
def convert_species_item(species_item, mb_groups):
"""
Make the conversion (type and/or format), for each species, between
the blocks of information encoded in the file globchem.dat and the
dictionary items used in pygchem.
"""
#species_item['absorption'] == bool(species_item['absorption'])
species_item['absorption'] = False # not used in GEOS-Chem
species_item['atomic_mass'] = float(species_item['atomic_mass'])
species_item['init_concentration'] = [
float(i) for i in species_item['init_concentration']
]
mb_vals = [int(i) for i in species_item['mb_groups']]
species_item['mb_groups'] = dict(zip(mb_groups.keys(), mb_vals))
def trim_rlist(reac_list):
"""
Take a 'reaction list' (e.g. reactants, products or stoichiometric
coefficients) and return a list with removed empty items
"""
# filter below permits to take only items that are not '' (if string)
# or 0 (if int or float) because bool('') and bool(0) both return False
return filter(bool, reac_list)
def read_reac(globchem_file, fline):
"""
Reads a 'chemical reaction' bloc of lines in
globchem.dat
Returns
-------
- reac_item: dict
an item of the reaction dictionnary (see ...)
"""
reac_r1_fmt = FortranRecordReader('(A1,1X,I4,1X,ES8.2,1X,ES8.1,1X,'
'I6,1X,I1,1X,A2,F6.2,1X,2(F6.0,1X),'
'A20)')
reac_r2_fmt = FortranRecordReader('(7X,ES8.2,1X,ES8.1,1X,I6,1X,I1,3X,'
'F6.2,1X,2(F6.0,1X))')
reac_eq_fmt = FortranRecordReader('(4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14))')
# re-arrange reaction rate parameters:
# parameter names for values (one-line) read in globchem.dat
# and correspondence between structure in globchem.dat and structure
# of pygchem.globchem module, depending on the reaction flag.
# note that reac_rates_keys are modified for additional lines of
# parameters (e.g., for line 1, 'AR' becomes 'AR1')
# TODO: move this information to a separate function to make it
# available to export functions
reac_rates_keys = ['AR', 'BR', 'CR', 'FCV', 'FCT1', 'FCT2']
mod_ratep = {
'': {
'arr': ['AR', 'BR', 'CR']
},
'P': {
'arrlow': ['AR', 'BR', 'CR'],
'arrhigh': ['AR1', 'BR1', 'CR1'],
'falloff': ['FCV', 'FCT1', 'FCT2']
},
'E': {
'arr': ['AR', 'BR', 'CR']
},
'X': {
'arrK0': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1'],
'arrK3': ['AR2', 'BR2', 'CR2']
},
'Y': {
'arrK0': ['AR', 'BR', 'CR']
},
'Z': {
'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']
},
'A': {
'arrK1': ['AR', 'BR', 'CR'],
'xcarbon': 'AR1'
},
'B': {
'arrK1': ['AR', 'BR', 'CR'],
'xcarbon': 'AR1'
},
'C': {
'arrK1': ['AR', 'BR', 'CR']
},
'D': {
'arrK1': ['AR', 'BR', 'CR']
},
'V': {
'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']
},
'G': {
'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']
},
}
# check if end of reaction list
l_globchem = globchem_file.readline().strip()
if (l_globchem[0:4] == "9999"):
fline += 1
return "end"
# read reaction info
reac_row1 = sanatize_str_inlist(reac_r1_fmt.read(l_globchem)) + [fline]
reac_item = [reac_row1[i] for i in [1, -1, 0, 6, -2]]
# read reaction rate parameters
n_addrates = reac_row1.pop(5)
reac_rates = dict(zip(reac_rates_keys,
reac_row1[2:5] + reac_row1[6:9]))
if (n_addrates > 0):
for i in range(0, n_addrates):
new_keys = [s + str(i + 1) for s in reac_rates_keys]
l_globchem = globchem_file.readline()
fline += 1
reac_row2 = reac_r2_fmt.read(l_globchem)
del reac_row2[3] # remove slot for number of rate coef lines
reac_rates.update(dict(zip(new_keys, reac_row2)))
# re-arrange rate parameters using corr_ratep
reac_flag = reac_item[3].upper()
mod_reac_rates = dict()
if reac_flag in mod_ratep:
for k, v in mod_ratep[reac_flag].items():
if (isinstance(v, collections.Iterable)
and not isinstance(v, basestring)):
mod_reac_rates[k] = [reac_rates[n] for n in v]
else:
mod_reac_rates[k] = reac_rates[v]
else:
mod_reac_rates.update(reac_rates)
reac_item.append(mod_reac_rates)
# read reaction equation
l_globchem = ""
for i in range(0, 5):
l_globchem += globchem_file.readline()
fline += 1
reac_eq = sanatize_str_inlist(reac_eq_fmt.read(l_globchem))
del reac_eq[0]
if (reac_eq[-2] is None):
reac_eq[-2] = 0.0
reac_item.append(trim_rlist([reac_eq[i] for i in xrange(1, 13, 3)]))
reac_item.append(trim_rlist([reac_eq[i] for i in xrange(13, 61, 3)]))
reac_item.append(trim_rlist([reac_eq[i] for i in range(12, 60, 3)]))
return reac_item
# path to additional info files
_dir_path = os.path.dirname(os.path.abspath(__file__))
finfo_path = os.path.join(_dir_path, "..", "data")
# read species.dat (get more info about species)
species_info = {}
s_fmt = FortranRecordReader('(A11,A32,A40)')
f_species_dat = open(os.path.join(finfo_path, "species.dat"), "r")
f_species_dat.readline()
for line in f_species_dat:
row = s_fmt.read(line)
row = [s.strip() for s in row]
species_info[row[0]] = row[1:]
f_species_dat.close()
species_info_blank = ['' for s in xrange(0, len(species_info.keys()[0]))]
# globchem.dat file
globchem_file = open(filename, "r")
# get header/comments of globchem.dat
fline = 1
species_subheader = _format_subheader("Species List")
header = go_2_begin(globchem_file, fline).replace(species_subheader, "")
# read in species
n_species = 0
# mass balance groups (id and status)
species_mb_id_fmt = FortranRecordReader('20X,A3,8(1X,A3)')
l_globchem = globchem_file.readline()
mb_id = sanatize_str_inlist(species_mb_id_fmt.read(l_globchem))
species_mb_st_fmt = FortranRecordReader('21X,A1,8(3X,A1)')
l_globchem = globchem_file.readline()
mb_st = sanatize_str_inlist(species_mb_st_fmt.read(l_globchem))
mb_groups = dict(zip(mb_id, mb_st))
fline += 2
species_r1_fmt = FortranRecordReader('(A1,1X,A14,A2,1X,0PF6.2,4(1PE10.3))')
while True:
l_globchem = globchem_file.readline().strip()
if (l_globchem == "END"):
break
species_r1 = sanatize_str_inlist(species_r1_fmt.read(l_globchem))
species_this_key = species_r1[1]
species_vals = ([n_species, fline] + species_r1[0:4] +
[species_r1[4:]] +
[[int(i) for i in globchem_file.readline().split()]])
try:
species_vals += species_info[species_this_key]
except KeyError:
species_vals += species_info_blank
species[species_this_key] = dict(zip(species_keys, species_vals))
convert_species_item(species[species_this_key], mb_groups)
del species_vals
n_species += 1
fline += 2
# read in reactions
go_2_begin(globchem_file, fline)
mem_p_ratep = dict()
n_reac = 0
while True:
reac_vals = read_reac(globchem_file, fline)
if (reac_vals == "end"):
break
else:
# case for reaction with E special flag (reverse equilibrium)
# --> add rate params of previous reaction with P flag
reac_flag = reac_vals[3]
if reac_flag == 'P':
mem_p_ratep = reac_vals[5]
elif reac_flag == 'E':
reac_vals[5].update(mem_p_ratep)
reac_kn[n_reac] = dict(zip(reac_keys, reac_vals))
reac_kn[n_reac]['id'] = n_reac
n_reac += 1
del reac_vals
go_2_begin(globchem_file, fline)
n_reac = 0
while True:
reac_vals = read_reac(globchem_file, fline)
if (reac_vals == "end"):
break
else:
reac_ph[n_reac] = dict(zip(reac_keys, reac_vals))
reac_ph[n_reac]['id'] = n_reac
n_reac += 1
del reac_vals
# identify links between species (through reactions): parse reac_kn
link_id = 0
for reac_key, reac_vals in reac_kn.iteritems():
for reactant in reac_vals['reactants']:
if (reactant != '' and reactant != 'M'):
for product in reac_vals['products']:
if (product != ''):
species_links.append(
(link_id, reac_key, reactant, product))
link_id += 1
# close globchem_file
globchem_file.close()
return header, mb_groups, species, reac_kn, reac_ph
def read_globchem_dat(filename):
"""
Read and parse the "globchem.dat" globchem_file (SMVGEARII syntax).
Parameters
----------
filename : string
Filename or path to the global chemistry globchem_file (globchem.dat)
Returns
-------
header : string
header (commented text) of the file
mb_groups : dict
mass balance groups (id, status): used for mass balance capability of
chemical solvers (SMVGEARII or KPP)
species : dict
chemical species
reac_kn : dict
list of chemical kinectic reactions
reac_ph : dict
list of photolysis reactions
species_links : list of tuples
links between species made by the kinectic reactions
"""
species = dict()
reac_kn = dict()
reac_ph = dict()
species_links = list()
# keys of 'species' and 'reac' dictionnaries
species_keys = ['ord_n', 'fline', 'status', 'id', 'absorption',
'atomic_mass', 'init_concentration', 'mb_groups',
'formula', 'name']
reac_keys = ['ord_n', 'fline', 'status', 'flag', 'comment',
'rate', 'reactants', 'products', 'coefs']
def sanatize_str_inlist(l):
"""
clean (strip...) string items in a list
"""
return([x.strip() if type(x) is str else x for x in l])
def go_2_begin(globchem_file, fline):
"""
jump lines in the text file until reading the line
with the word "BEGIN"
"""
jumptext = ""
while True:
text = globchem_file.readline().strip()
fline += 1
if(text == "BEGIN"):
break
else:
jumptext += text + '\n'
return jumptext
def convert_species_item(species_item, mb_groups):
"""
Make the conversion (type and/or format), for each species, between
the blocks of information encoded in the file globchem.dat and the
dictionary items used in pygchem.
"""
#species_item['absorption'] == bool(species_item['absorption'])
species_item['absorption'] = False # not used in GEOS-Chem
species_item['atomic_mass'] = float(species_item['atomic_mass'])
species_item['init_concentration'] = [float(i) for i in
species_item['init_concentration']]
mb_vals = [int(i) for i in species_item['mb_groups']]
species_item['mb_groups'] = dict(zip(mb_groups.keys(), mb_vals))
def trim_rlist(reac_list):
"""
Take a 'reaction list' (e.g. reactants, products or stoichiometric
coefficients) and return a list with removed empty items
"""
# filter below permits to take only items that are not '' (if string)
# or 0 (if int or float) because bool('') and bool(0) both return False
return filter(bool, reac_list)
def read_reac(globchem_file, fline):
"""
Reads a 'chemical reaction' bloc of lines in
globchem.dat
Returns
-------
- reac_item: dict
an item of the reaction dictionnary (see ...)
"""
reac_r1_fmt = FortranRecordReader('(A1,1X,I4,1X,ES8.2,1X,ES8.1,1X,'
'I6,1X,I1,1X,A2,F6.2,1X,2(F6.0,1X),'
'A20)')
reac_r2_fmt = FortranRecordReader('(7X,ES8.2,1X,ES8.1,1X,I6,1X,I1,3X,'
'F6.2,1X,2(F6.0,1X))')
reac_eq_fmt = FortranRecordReader('(4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14))')
# re-arrange reaction rate parameters:
# parameter names for values (one-line) read in globchem.dat
# and correspondence between structure in globchem.dat and structure
# of pygchem.globchem module, depending on the reaction flag.
# note that reac_rates_keys are modified for additional lines of
# parameters (e.g., for line 1, 'AR' becomes 'AR1')
# TODO: move this information to a separate function to make it
# available to export functions
reac_rates_keys = ['AR', 'BR', 'CR', 'FCV', 'FCT1', 'FCT2']
mod_ratep = {'' : {'arr': ['AR', 'BR', 'CR']},
'P': {'arrlow': ['AR', 'BR', 'CR'],
'arrhigh': ['AR1', 'BR1', 'CR1'],
'falloff': ['FCV', 'FCT1', 'FCT2']},
'E': {'arr': ['AR', 'BR', 'CR']},
'X': {'arrK0': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1'],
'arrK3': ['AR2', 'BR2', 'CR2']},
'Y': {'arrK0': ['AR', 'BR', 'CR']},
'Z': {'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']},
'A': {'arrK1': ['AR', 'BR', 'CR'],
'xcarbon': 'AR1'},
'B': {'arrK1': ['AR', 'BR', 'CR'],
'xcarbon': 'AR1'},
'C': {'arrK1': ['AR', 'BR', 'CR']},
'D': {'arrK1': ['AR', 'BR', 'CR']},
'V': {'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']},
'G': {'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']},
}
# check if end of reaction list
l_globchem = globchem_file.readline().strip()
if(l_globchem[0:4] == "9999"):
fline += 1
return "end"
# read reaction info
reac_row1 = sanatize_str_inlist(reac_r1_fmt.read(l_globchem)) + [fline]
reac_item = [reac_row1[i] for i in [1, -1, 0, 6, -2]]
# read reaction rate parameters
n_addrates = reac_row1.pop(5)
reac_rates = dict(zip(reac_rates_keys,
reac_row1[2:5] + reac_row1[6:9]))
if(n_addrates > 0):
for i in range(0, n_addrates):
new_keys = [s + str(i + 1) for s in reac_rates_keys]
l_globchem = globchem_file.readline()
fline += 1
reac_row2 = reac_r2_fmt.read(l_globchem)
del reac_row2[3] # remove slot for number of rate coef lines
reac_rates.update(dict(zip(new_keys, reac_row2)))
# re-arrange rate parameters using corr_ratep
reac_flag = reac_item[3].upper()
mod_reac_rates = dict()
if reac_flag in mod_ratep:
for k, v in mod_ratep[reac_flag].items():
if (isinstance(v, collections.Iterable)
and not isinstance(v, basestring)):
mod_reac_rates[k] = [reac_rates[n] for n in v]
else:
mod_reac_rates[k] = reac_rates[v]
else:
mod_reac_rates.update(reac_rates)
reac_item.append(mod_reac_rates)
# read reaction equation
l_globchem = ""
for i in range(0, 5):
l_globchem += globchem_file.readline()
fline += 1
reac_eq = sanatize_str_inlist(reac_eq_fmt.read(l_globchem))
del reac_eq[0]
if(reac_eq[-2] is None):
reac_eq[-2] = 0.0
reac_item.append(trim_rlist([reac_eq[i] for i in xrange(1, 13, 3)]))
reac_item.append(trim_rlist([reac_eq[i] for i in xrange(13, 61, 3)]))
reac_item.append(trim_rlist([reac_eq[i] for i in range(12, 60, 3)]))
return reac_item
# path to additional info files
_dir_path = os.path.dirname(os.path.abspath(__file__))
finfo_path = os.path.join(_dir_path, "..", "data")
# read species.dat (get more info about species)
species_info = {}
s_fmt = FortranRecordReader('(A11,A32,A40)')
f_species_dat = open(os.path.join(finfo_path, "species.dat"), "r")
f_species_dat.readline()
for line in f_species_dat:
row = s_fmt.read(line)
row = [s.strip() for s in row]
species_info[row[0]] = row[1:]
f_species_dat.close()
species_info_blank = ['' for s in xrange(0, len(species_info.keys()[0]))]
# globchem.dat file
globchem_file = open(filename, "r")
# get header/comments of globchem.dat
fline = 1
species_subheader = _format_subheader("Species List")
header = go_2_begin(globchem_file, fline).replace(species_subheader, "")
# read in species
n_species = 0
# mass balance groups (id and status)
species_mb_id_fmt = FortranRecordReader('20X,A3,8(1X,A3)')
l_globchem = globchem_file.readline()
mb_id = sanatize_str_inlist(species_mb_id_fmt.read(l_globchem))
species_mb_st_fmt = FortranRecordReader('21X,A1,8(3X,A1)')
l_globchem = globchem_file.readline()
mb_st = sanatize_str_inlist(species_mb_st_fmt.read(l_globchem))
mb_groups = dict(zip(mb_id, mb_st))
fline += 2
species_r1_fmt = FortranRecordReader('(A1,1X,A14,A2,1X,0PF6.2,4(1PE10.3))')
while True:
l_globchem = globchem_file.readline().strip()
if(l_globchem == "END"):
break
species_r1 = sanatize_str_inlist(species_r1_fmt.read(l_globchem))
species_this_key = species_r1[1]
species_vals = ([n_species, fline] +
species_r1[0:4] +
[species_r1[4:]] +
[[int(i) for i in globchem_file.readline().split()]])
try:
species_vals += species_info[species_this_key]
except KeyError:
species_vals += species_info_blank
species[species_this_key] = dict(zip(species_keys, species_vals))
convert_species_item(species[species_this_key], mb_groups)
del species_vals
n_species += 1
fline += 2
# read in reactions
go_2_begin(globchem_file, fline)
mem_p_ratep = dict()
n_reac = 0
while True:
reac_vals = read_reac(globchem_file, fline)
if(reac_vals == "end"):
break
else:
# case for reaction with E special flag (reverse equilibrium)
# --> add rate params of previous reaction with P flag
reac_flag = reac_vals[3]
if reac_flag == 'P':
mem_p_ratep = reac_vals[5]
elif reac_flag == 'E':
reac_vals[5].update(mem_p_ratep)
reac_kn[n_reac] = dict(zip(reac_keys, reac_vals))
reac_kn[n_reac]['id'] = n_reac
n_reac += 1
del reac_vals
go_2_begin(globchem_file, fline)
n_reac = 0
while True:
reac_vals = read_reac(globchem_file, fline)
if(reac_vals == "end"):
break
else:
reac_ph[n_reac] = dict(zip(reac_keys, reac_vals))
reac_ph[n_reac]['id'] = n_reac
n_reac += 1
del reac_vals
# identify links between species (through reactions): parse reac_kn
link_id = 0
for reac_key, reac_vals in reac_kn.iteritems():
for reactant in reac_vals['reactants']:
if(reactant != '' and reactant != 'M'):
for product in reac_vals['products']:
if(product != ''):
species_links.append((link_id, reac_key,
reactant, product))
link_id += 1
# close globchem_file
globchem_file.close()
return header, mb_groups, species, reac_kn, reac_ph
def read_reac(globchem_file, fline):
"""
Reads a 'chemical reaction' bloc of lines in
globchem.dat
Returns
-------
- reac_item: dict
an item of the reaction dictionnary (see ...)
"""
reac_r1_fmt = FortranRecordReader('(A1,1X,I4,1X,ES8.2,1X,ES8.1,1X,'
'I6,1X,I1,1X,A2,F6.2,1X,2(F6.0,1X),'
'A20)')
reac_r2_fmt = FortranRecordReader('(7X,ES8.2,1X,ES8.1,1X,I6,1X,I1,3X,'
'F6.2,1X,2(F6.0,1X))')
reac_eq_fmt = FortranRecordReader('(4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14))')
# re-arrange reaction rate parameters:
# parameter names for values (one-line) read in globchem.dat
# and correspondence between structure in globchem.dat and structure
# of pygchem.globchem module, depending on the reaction flag.
# note that reac_rates_keys are modified for additional lines of
# parameters (e.g., for line 1, 'AR' becomes 'AR1')
# TODO: move this information to a separate function to make it
# available to export functions
reac_rates_keys = ['AR', 'BR', 'CR', 'FCV', 'FCT1', 'FCT2']
mod_ratep = {
'': {
'arr': ['AR', 'BR', 'CR']
},
'P': {
'arrlow': ['AR', 'BR', 'CR'],
'arrhigh': ['AR1', 'BR1', 'CR1'],
'falloff': ['FCV', 'FCT1', 'FCT2']
},
'E': {
'arr': ['AR', 'BR', 'CR']
},
'X': {
'arrK0': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1'],
'arrK3': ['AR2', 'BR2', 'CR2']
},
'Y': {
'arrK0': ['AR', 'BR', 'CR']
},
'Z': {
'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']
},
'A': {
'arrK1': ['AR', 'BR', 'CR'],
'xcarbon': 'AR1'
},
'B': {
'arrK1': ['AR', 'BR', 'CR'],
'xcarbon': 'AR1'
},
'C': {
'arrK1': ['AR', 'BR', 'CR']
},
'D': {
'arrK1': ['AR', 'BR', 'CR']
},
'V': {
'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']
},
'G': {
'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']
},
}
# check if end of reaction list
l_globchem = globchem_file.readline().strip()
if (l_globchem[0:4] == "9999"):
fline += 1
return "end"
# read reaction info
reac_row1 = sanatize_str_inlist(reac_r1_fmt.read(l_globchem)) + [fline]
reac_item = [reac_row1[i] for i in [1, -1, 0, 6, -2]]
# read reaction rate parameters
n_addrates = reac_row1.pop(5)
reac_rates = dict(zip(reac_rates_keys,
reac_row1[2:5] + reac_row1[6:9]))
if (n_addrates > 0):
for i in range(0, n_addrates):
new_keys = [s + str(i + 1) for s in reac_rates_keys]
l_globchem = globchem_file.readline()
fline += 1
reac_row2 = reac_r2_fmt.read(l_globchem)
del reac_row2[3] # remove slot for number of rate coef lines
reac_rates.update(dict(zip(new_keys, reac_row2)))
# re-arrange rate parameters using corr_ratep
reac_flag = reac_item[3].upper()
mod_reac_rates = dict()
if reac_flag in mod_ratep:
for k, v in mod_ratep[reac_flag].items():
if (isinstance(v, collections.Iterable)
and not isinstance(v, basestring)):
mod_reac_rates[k] = [reac_rates[n] for n in v]
else:
mod_reac_rates[k] = reac_rates[v]
else:
mod_reac_rates.update(reac_rates)
reac_item.append(mod_reac_rates)
# read reaction equation
l_globchem = ""
for i in range(0, 5):
l_globchem += globchem_file.readline()
fline += 1
reac_eq = sanatize_str_inlist(reac_eq_fmt.read(l_globchem))
del reac_eq[0]
if (reac_eq[-2] is None):
reac_eq[-2] = 0.0
reac_item.append(trim_rlist([reac_eq[i] for i in xrange(1, 13, 3)]))
reac_item.append(trim_rlist([reac_eq[i] for i in xrange(13, 61, 3)]))
reac_item.append(trim_rlist([reac_eq[i] for i in range(12, 60, 3)]))
return reac_item
def read_reac(globchem_file, fline):
"""
Reads a 'chemical reaction' bloc of lines in
globchem.dat
Returns
-------
- reac_item: dict
an item of the reaction dictionnary (see ...)
"""
reac_r1_fmt = FortranRecordReader('(A1,1X,I4,1X,ES8.2,1X,ES8.1,1X,'
'I6,1X,I1,1X,A2,F6.2,1X,2(F6.0,1X),'
'A20)')
reac_r2_fmt = FortranRecordReader('(7X,ES8.2,1X,ES8.1,1X,I6,1X,I1,3X,'
'F6.2,1X,2(F6.0,1X))')
reac_eq_fmt = FortranRecordReader('(4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14)/'
'4(A1,0PF5.3,A14))')
# re-arrange reaction rate parameters:
# parameter names for values (one-line) read in globchem.dat
# and correspondence between structure in globchem.dat and structure
# of pygchem.globchem module, depending on the reaction flag.
# note that reac_rates_keys are modified for additional lines of
# parameters (e.g., for line 1, 'AR' becomes 'AR1')
# TODO: move this information to a separate function to make it
# available to export functions
reac_rates_keys = ['AR', 'BR', 'CR', 'FCV', 'FCT1', 'FCT2']
mod_ratep = {'' : {'arr': ['AR', 'BR', 'CR']},
'P': {'arrlow': ['AR', 'BR', 'CR'],
'arrhigh': ['AR1', 'BR1', 'CR1'],
'falloff': ['FCV', 'FCT1', 'FCT2']},
'E': {'arr': ['AR', 'BR', 'CR']},
'X': {'arrK0': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1'],
'arrK3': ['AR2', 'BR2', 'CR2']},
'Y': {'arrK0': ['AR', 'BR', 'CR']},
'Z': {'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']},
'A': {'arrK1': ['AR', 'BR', 'CR'],
'xcarbon': 'AR1'},
'B': {'arrK1': ['AR', 'BR', 'CR'],
'xcarbon': 'AR1'},
'C': {'arrK1': ['AR', 'BR', 'CR']},
'D': {'arrK1': ['AR', 'BR', 'CR']},
'V': {'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']},
'G': {'arrK1': ['AR', 'BR', 'CR'],
'arrK2': ['AR1', 'BR1', 'CR1']},
}
# check if end of reaction list
l_globchem = globchem_file.readline().strip()
if(l_globchem[0:4] == "9999"):
fline += 1
return "end"
# read reaction info
reac_row1 = sanatize_str_inlist(reac_r1_fmt.read(l_globchem)) + [fline]
reac_item = [reac_row1[i] for i in [1, -1, 0, 6, -2]]
# read reaction rate parameters
n_addrates = reac_row1.pop(5)
reac_rates = dict(zip(reac_rates_keys,
reac_row1[2:5] + reac_row1[6:9]))
if(n_addrates > 0):
for i in range(0, n_addrates):
new_keys = [s + str(i + 1) for s in reac_rates_keys]
l_globchem = globchem_file.readline()
fline += 1
reac_row2 = reac_r2_fmt.read(l_globchem)
del reac_row2[3] # remove slot for number of rate coef lines
reac_rates.update(dict(zip(new_keys, reac_row2)))
# re-arrange rate parameters using corr_ratep
reac_flag = reac_item[3].upper()
mod_reac_rates = dict()
if reac_flag in mod_ratep:
for k, v in mod_ratep[reac_flag].items():
if (isinstance(v, collections.Iterable)
and not isinstance(v, basestring)):
mod_reac_rates[k] = [reac_rates[n] for n in v]
else:
mod_reac_rates[k] = reac_rates[v]
else:
mod_reac_rates.update(reac_rates)
reac_item.append(mod_reac_rates)
# read reaction equation
l_globchem = ""
for i in range(0, 5):
l_globchem += globchem_file.readline()
fline += 1
reac_eq = sanatize_str_inlist(reac_eq_fmt.read(l_globchem))
del reac_eq[0]
if(reac_eq[-2] is None):
reac_eq[-2] = 0.0
reac_item.append(trim_rlist([reac_eq[i] for i in xrange(1, 13, 3)]))
reac_item.append(trim_rlist([reac_eq[i] for i in xrange(13, 61, 3)]))
reac_item.append(trim_rlist([reac_eq[i] for i in range(12, 60, 3)]))
return reac_item
