def chem_scheme_SMILES_extr(sch_name, xml_name, chem_scheme_markers):
# inputs: ------------------------------------------
# sch_name - path to chemical scheme
# xml_name - path to xml name
# chem_scheme_markers - markers for chemical scheme
# ----------------------------------------------------
# initiate with empty error message
err_mess = ''
f_open_eqn = open(sch_name, mode='r') # open the chemical scheme file
# read the file and store everything into a list
total_list_eqn = f_open_eqn.readlines()
f_open_eqn.close() # close file
# interrogate scheme to list equations
[eqn_list, aqeqn_list, eqn_num, rrc, rrc_name,
RO2_names] = sch_interr.sch_interr(total_list_eqn, chem_scheme_markers)
# interrogate xml to list all component names and SMILES
[comp_smil, comp_name] = xml_interr.xml_interr(xml_name)
comp_namelist = [
] # list for chemical scheme names of components in the chemical scheme
comp_list = [
] # list for the SMILE strings of components present in the chemical scheme
for eqn_step in range(eqn_num[0]): # loop through gas-phase reactions
line = eqn_list[eqn_step] # extract this line
# work out whether equation or reaction rate coefficient part comes first
eqn_start = str('.*\\' + chem_scheme_markers[10])
rrc_start = str('.*\\' + chem_scheme_markers[9])
# get index of these markers, note span is the property of the match object that
# gives the location of the marker
eqn_start_indx = (re.match(eqn_start, line)).span()[1]
rrc_start_indx = (re.match(rrc_start, line)).span()[1]
if (eqn_start_indx > rrc_start_indx):
eqn_sec = 1 # equation is second part
else:
eqn_sec = 0 # equation is first part
# split the line into 2 parts: equation and rate coefficient
# . means match with anything except a new line character., when followed by a *
# means match zero or more times (so now we match with all characters in the line
# except for new line characters, so final part is stating the character(s) we
# are specifically looking for, \\ ensures the marker is recognised
if eqn_sec == 1:
eqn_markers = str('\\' + chem_scheme_markers[10] + '.*\\' +
chem_scheme_markers[11])
else: # end of equation part is start of reaction rate coefficient part
eqn_markers = str('\\' + chem_scheme_markers[10] + '.*\\' +
chem_scheme_markers[9])
# extract the equation as a string ([0] extracts the equation section and
# [1:-1] removes the bounding markers)
eqn = re.findall(eqn_markers, line)[0][1:-1].strip()
eqn_split = eqn.split()
eqmark_pos = eqn_split.index('=')
# reactants with stoichiometry number and omit any photon
reactants = [
i for i in eqn_split[:eqmark_pos] if i != '+' and i != 'hv'
]
# products with stoichiometry number
products = [t for t in eqn_split[eqmark_pos + 1:] if t != '+']
stoich_regex = r"^\d*\.\d*|^\d*" # necessary for checking for stoichiometries
for reactant in reactants: # left hand side of equations (losses)
if (re.findall(stoich_regex, reactant)[0] !=
''): # when stoichiometry included
# name with no stoichiometry number
name_only = re.sub(stoich_regex, '', reactant)
elif (re.findall(
stoich_regex,
reactant)[0] == ''): # when stoichiometry excluded
name_only = reactant
if (name_only
not in comp_namelist): # if new component encountered
comp_namelist.append(
name_only) # add to chemical scheme name list
# convert MCM chemical names to SMILES
if (name_only in comp_name):
# index where xml file name matches reaction component name
name_indx = comp_name.index(name_only)
name_SMILE = comp_smil[name_indx] # SMILES of component
comp_list.append(name_SMILE) # list SMILE names
else:
err_mess = str('Error - chemical scheme name ' +
str(name_only) + ' not found in xml file')
return (comp_namelist, comp_list, err_mess, H2Oi)
for product in products: # right hand side of equations (gains)
if (re.findall(stoich_regex, product)[0] !=
''): # when stoichiometry included
# name with no stoichiometry number
name_only = re.sub(stoich_regex, '', product)
elif (re.findall(stoich_regex,
product)[0] == ''): # when stoichiometry excluded
name_only = product
if (name_only
not in comp_namelist): # if new component encountered
comp_namelist.append(
name_only) # add to chemical scheme name list
# convert MCM chemical names to SMILES
# index where xml file name matches reaction component name
if name_only in comp_name:
name_indx = comp_name.index(name_only)
name_SMILE = comp_smil[name_indx]
comp_list.append(name_SMILE) # list SMILE names
else:
err_mess = str('Error - chemical scheme name ' +
str(name_only) + ' not found in xml file')
return (comp_namelist, comp_list, err_mess, H2Oi)
# check for water presence in chemical scheme via its SMILE string
# count on components
indx = -1
for single_chem in comp_list:
indx += 1
# ensure this is water rather than single oxygen (e.g. due to ozone photolysis
# (O is the MCM chemical scheme name for single oxygen))
if (single_chem == 'O' and comp_namelist[indx] != 'O'):
H2Oi = indx
else: # if not in chemical scheme, water would be the next component appended to component list
H2Oi = len(comp_list)
comp_namelist.append('H2O')
return (comp_namelist, comp_list, err_mess, H2Oi)
def extr_mech(sch_name, chem_sch_mrk, xml_name, photo_path, con_infl_nam,
int_tol, wall_on, num_sb, const_comp, drh_str, erh_str):
# inputs: ----------------------------------------------------
# sch_name - file name of chemical scheme
# chem_sch_mrk - markers to identify different sections of
# the chemical scheme
# xml_name - name of xml file
# photo_path - path to file containing absorption
# cross-sections and quantum yields
# con_infl_nam - chemical scheme names of components with
# constant influx
# int_tol - integration tolerances
# wall_on - marker for whether to include wall partitioning
# num_sb - number of size bins (including any wall)
# const_comp - chemical scheme name of components with
# constant concentration
# drh_str - string from user inputs describing
# deliquescence RH (fraction 0-1) as function of temperature (K)
# erh_str - string from user inputs describing
# efflorescence RH (fraction 0-1) as function of temperature (K)
# ------------------------------------------------------------
f_open_eqn = open(sch_name, mode='r') # open the chemical scheme file
# read the file and store everything into a list
total_list_eqn = f_open_eqn.readlines()
f_open_eqn.close() # close file
# interrogate scheme to list equations
[eqn_list, aqeqn_list, eqn_num, rrc, rrc_name,
RO2_names] = sch_interr.sch_interr(total_list_eqn, chem_sch_mrk)
# interrogate xml to list all component names and SMILES
[comp_smil, comp_name] = xml_interr.xml_interr(xml_name)
# get equation information for chemical reactions
[
rindx_g, rstoi_g, pindx_g, pstoi_g, reac_coef_g, nreac_g, nprod_g,
jac_stoi_g, jac_den_indx_g, njac_g, jac_indx_g, y_arr_g, y_rind_g,
uni_y_rind_g, y_pind_g, uni_y_pind_g, reac_col_g, prod_col_g,
rstoi_flat_g, pstoi_flat_g, rr_arr_g, rr_arr_p_g, rindx_aq, rstoi_aq,
pindx_aq, pstoi_aq, reac_coef_aq, nreac_aq, nprod_aq, jac_stoi_aq,
jac_den_indx_aq, njac_aq, jac_indx_aq, y_arr_aq, y_rind_aq,
uni_y_rind_aq, y_pind_aq, uni_y_pind_aq, reac_col_aq, prod_col_aq,
rstoi_flat_aq, pstoi_flat_aq, rr_arr_aq, rr_arr_p_aq, comp_namelist,
comp_list, Pybel_objects, comp_num
] = eqn_interr.eqn_interr(eqn_num, eqn_list, aqeqn_list, chem_sch_mrk,
comp_name, comp_smil, num_sb, wall_on)
[rowvals, colptrs, jac_indx_g, jac_indx_aq, jac_part_indx, jac_wall_indx
] = jac_setup.jac_setup(jac_den_indx_g, njac_g, comp_num, num_sb, eqn_num,
nreac_g, nprod_g, rindx_g, pindx_g, jac_indx_g,
wall_on, nreac_aq, nprod_aq, rindx_aq, pindx_aq,
jac_indx_aq, (num_sb - wall_on))
# prepare aqueous-phase reaction matrices for applying to reaction rate calculation
if (eqn_num[1] > 0): # if aqueous-phase reactions present
[
rindx_aq, rstoi_aq, pindx_aq, pstoi_aq, reac_coef_aq, nprod_aq,
jac_stoi_aq, njac_aq, jac_den_indx_aq, jac_indx_aq, y_arr_aq,
y_rind_aq, uni_y_rind_aq, y_pind_aq, uni_y_pind_aq, reac_col_aq,
prod_col_aq, rstoi_flat_aq, pstoi_flat_aq, rr_arr_aq, rr_arr_p_aq
] = aq_mat_prep.aq_mat_prep(
rindx_aq, rstoi_aq, pindx_aq, pstoi_aq, reac_coef_aq, nprod_aq,
jac_stoi_aq, njac_aq, jac_den_indx_aq, jac_indx_aq, y_arr_aq,
y_rind_aq, uni_y_rind_aq, y_pind_aq, uni_y_pind_aq, reac_col_aq,
prod_col_aq, rstoi_flat_aq, pstoi_flat_aq, rr_arr_aq, rr_arr_p_aq,
num_sb, wall_on, eqn_num[1], comp_num)
# get index of components with constant influx/concentration -----------
# empty array for storing index of components with constant influx
con_infl_indx = np.zeros((len(con_infl_nam)))
con_C_indx = np.zeros((len(const_comp)))
for i in range(len(con_infl_nam)):
# index of where constant components occur in list of components
con_infl_indx[i] = comp_namelist.index(con_infl_nam[i])
for i in range(len(const_comp)):
# index of where constant concnetration components occur in list
# of components
con_C_indx[i] = comp_namelist.index(const_comp[i])
# ---------------------------------------------------------------------
# call function to generate ordinary differential equation (ODE)
# solver module, add two to comp_num to account for water and core component
write_ode_solv.ode_gen(con_infl_indx, int_tol, rowvals, wall_on,
comp_num + 2, (num_sb - wall_on), con_C_indx, 0,
eqn_num)
# call function to generate reaction rate calculation module
write_rate_file.write_rate_file(reac_coef_g, reac_coef_aq, rrc, rrc_name,
0)
# call function to generate module that tracks change tendencies
# of certain components
write_dydt_rec.write_dydt_rec()
# write the module for estimating deliquescence and efflorescence
# relative humidities as a function of temperature
write_hyst_eq.write_hyst_eq(drh_str, erh_str)
# get index of components in the peroxy radical list
RO2_indx = RO2_indices.RO2_indices(comp_namelist, RO2_names)
# get number of photolysis equations
Jlen = photo_num.photo_num(photo_path)
return (rindx_g, pindx_g, rstoi_g, pstoi_g, nreac_g, nprod_g, jac_stoi_g,
njac_g, jac_den_indx_g, jac_indx_g, y_arr_g, y_rind_g,
uni_y_rind_g, y_pind_g, uni_y_pind_g, reac_col_g, prod_col_g,
rstoi_flat_g, pstoi_flat_g, rr_arr_g, rr_arr_p_g, rowvals, colptrs,
jac_wall_indx, jac_part_indx, comp_num, RO2_indx, comp_list,
Pybel_objects, eqn_num, comp_namelist, Jlen, rindx_aq, rstoi_aq,
pindx_aq, pstoi_aq, reac_coef_aq, nreac_aq, nprod_aq, jac_stoi_aq,
jac_den_indx_aq, njac_aq, jac_indx_aq, y_arr_aq, y_rind_aq,
uni_y_rind_aq, y_pind_aq, uni_y_pind_aq, reac_col_aq, prod_col_aq,
rstoi_flat_aq, pstoi_flat_aq, rr_arr_aq, rr_arr_p_aq, comp_name,
comp_smil)
except: # when calling from GMD paper Results folder output_by_sim = str(cwd + '/fig07_data/Gaswall_sens_Cw0_kw1e2') # required outputs (num_sb, num_comp, Cfac, y, Ndry, rbou_rec, xfm, t_array, comp_names, y_mw, N, _, y_MV, _, wall_on, space_mode) = retr_out.retr_out(output_by_sim) # required outputs from full-moving (num_sb, num_comp, Cfac, y, Ndry, rbou_rec, xfm, t_array, comp_names, y_mw, N, _, y_MV, _, wall_on, space_mode) = retr_out.retr_out(output_by_sim) # get all SMILE strings from the xml file # interrogate xml to list component names and SMILES try: # when calling from the PyCHAM home directory [comp_smil, comp_name] = xml_interr.xml_interr(str(cwd + '/PyCHAM/input/example_xml.xml')) except: # when calling from the GMD paper Results folder [comp_smil, comp_name] = xml_interr.xml_interr(str(cwd + '/example_xml.xml')) # convert chemical scheme component names into SMILEs comp_smiles = [] # holder for name in comp_names[0:-2]: # omit H20 and core at end of comp_names comp_smiles.append(comp_smil[comp_name.index(name)]) SOA0 = 0. for i in range(1, num_sb): # calculate SOA (*1.0E-12 to convert from g/cc (air) to ug/m3 (air)) SOA0 += (((y[:, num_comp*i:num_comp*(i+1)-2]/si.N_A)*y_mw[0:-2]*1.0e12).sum(axis=1)) Pybel_objects = [] # holder for Pybel object names for i in range(num_comp-2): # component loop
def extr_mech(sch_name, chem_sch_mrk, xml_name, photo_path, con_infl_nam,
int_tol, wall_on, num_sb, const_comp, drh_str, erh_str, dil_fac,
sav_nam, pcont):
# inputs: ----------------------------------------------------
# sch_name - file name of chemical scheme
# chem_sch_mrk - markers to identify different sections of
# the chemical scheme
# xml_name - name of xml file
# photo_path - path to file containing absorption
# cross-sections and quantum yields
# con_infl_nam - chemical scheme names of components with
# constant influx
# int_tol - integration tolerances
# wall_on - marker for whether to include wall partitioning
# num_sb - number of size bins (including any wall)
# const_comp - chemical scheme name of components with
# constant concentration
# drh_str - string from user inputs describing
# deliquescence RH (fraction 0-1) as function of temperature (K)
# erh_str - string from user inputs describing
# efflorescence RH (fraction 0-1) as function of temperature (K)
# dil_fac - fraction of chamber air extracted/s
# sav_nam - name of folder to save results to
# pcont - flag for whether seed particle injection is
# instantaneous (0) or continuous (1)
# ------------------------------------------------------------
# starting error flag and message (assumes no errors)
erf = 0
err_mess = ''
f_open_eqn = open(sch_name, mode='r') # open the chemical scheme file
# read the file and store everything into a list
total_list_eqn = f_open_eqn.readlines()
f_open_eqn.close() # close file
# interrogate scheme to list equations
[eqn_list, aqeqn_list, eqn_num, rrc, rrc_name,
RO2_names] = sch_interr.sch_interr(total_list_eqn, chem_sch_mrk)
# interrogate xml to list all component names and SMILES
[comp_smil, comp_name] = xml_interr.xml_interr(xml_name)
# get equation information for chemical reactions
[
rindx_g, rstoi_g, pindx_g, pstoi_g, reac_coef_g, nreac_g, nprod_g,
jac_stoi_g, jac_den_indx_g, njac_g, jac_indx_g, y_arr_g, y_rind_g,
uni_y_rind_g, y_pind_g, uni_y_pind_g, reac_col_g, prod_col_g,
rstoi_flat_g, pstoi_flat_g, rr_arr_g, rr_arr_p_g, rindx_aq, rstoi_aq,
pindx_aq, pstoi_aq, reac_coef_aq, nreac_aq, nprod_aq, jac_stoi_aq,
jac_den_indx_aq, njac_aq, jac_indx_aq, y_arr_aq, y_rind_aq,
uni_y_rind_aq, y_pind_aq, uni_y_pind_aq, reac_col_aq, prod_col_aq,
rstoi_flat_aq, pstoi_flat_aq, rr_arr_aq, rr_arr_p_aq, comp_namelist,
comp_list, Pybel_objects, comp_num, RO_indx
] = eqn_interr.eqn_interr(eqn_num, eqn_list, aqeqn_list, chem_sch_mrk,
comp_name, comp_smil, num_sb, wall_on)
[
rowvals, colptrs, jac_indx_g, jac_indx_aq, jac_part_indx,
jac_wall_indx, jac_extr_indx
] = jac_setup.jac_setup(jac_den_indx_g, njac_g, comp_num, num_sb, eqn_num,
nreac_g, nprod_g, rindx_g, pindx_g, jac_indx_g,
wall_on, nreac_aq, nprod_aq, rindx_aq, pindx_aq,
jac_indx_aq, (num_sb - wall_on), dil_fac)
# prepare aqueous-phase reaction matrices for applying to reaction rate calculation
if (eqn_num[1] > 0): # if aqueous-phase reactions present
[
rindx_aq, rstoi_aq, pindx_aq, pstoi_aq, reac_coef_aq, nprod_aq,
jac_stoi_aq, njac_aq, jac_den_indx_aq, jac_indx_aq, y_arr_aq,
y_rind_aq, uni_y_rind_aq, y_pind_aq, uni_y_pind_aq, reac_col_aq,
prod_col_aq, rstoi_flat_aq, pstoi_flat_aq, rr_arr_aq, rr_arr_p_aq
] = aq_mat_prep.aq_mat_prep(
rindx_aq, rstoi_aq, pindx_aq, pstoi_aq, reac_coef_aq, nprod_aq,
jac_stoi_aq, njac_aq, jac_den_indx_aq, jac_indx_aq, y_arr_aq,
y_rind_aq, uni_y_rind_aq, y_pind_aq, uni_y_pind_aq, reac_col_aq,
prod_col_aq, rstoi_flat_aq, pstoi_flat_aq, rr_arr_aq, rr_arr_p_aq,
num_sb, wall_on, eqn_num[1], comp_num)
# get index of components with constant influx/concentration -----------
# empty array for storing index of components with constant influx
con_infl_indx = np.zeros((len(con_infl_nam)))
con_C_indx = np.zeros((len(const_comp))).astype('int')
for i in range(len(con_infl_nam)):
# water not included explicitly in chemical schemes but accounted for later in init_conc
if (con_infl_nam[i] == 'H2O'):
con_infl_indx[i] = comp_num
continue
try:
# index of where components with constant influx occur in list of components
con_infl_indx[i] = comp_namelist.index(con_infl_nam[i])
except:
erf = 1 # raise error
err_mess = str(
'Error: constant influx component with name ' +
str(con_infl_nam[i]) +
' has not been identified in the chemical scheme, please check it is present and the chemical scheme markers are correct'
)
for i in range(len(const_comp)):
try:
# index of where constant concentration components occur in list
# of components
con_C_indx[i] = comp_namelist.index(const_comp[i])
except:
erf = 1 # raise error
err_mess = str(
'Error: constant concentration component with name ' +
str(const_comp[i]) +
' has not been identified in the chemical scheme, please check it is present and the chemical scheme markers are correct'
)
# ---------------------------------------------------------------------
# call function to generate ordinary differential equation (ODE)
# solver module, add two to comp_num to account for water and core component
write_ode_solv.ode_gen(con_infl_indx, int_tol, rowvals, wall_on,
comp_num + 2, (num_sb - wall_on), 0, eqn_num,
dil_fac, sav_nam, pcont)
# call function to generate reaction rate calculation module
write_rate_file.write_rate_file(reac_coef_g, reac_coef_aq, rrc, rrc_name,
0)
# call function to generate module that tracks change tendencies
# of certain components
write_dydt_rec.write_dydt_rec()
# write the module for estimating deliquescence and efflorescence
# relative humidities as a function of temperature
write_hyst_eq.write_hyst_eq(drh_str, erh_str)
# get index of components in the peroxy radical list
RO2_indx = RO2_indices.RO2_indices(comp_namelist, RO2_names)
# get index of HOM-RO2 radicals
HOMRO2_indx = RO2_indices.HOMRO2_indices(comp_namelist)
# get number of photolysis equations
Jlen = photo_num.photo_num(photo_path)
return (rindx_g, pindx_g, rstoi_g, pstoi_g, nreac_g, nprod_g, jac_stoi_g,
njac_g, jac_den_indx_g, jac_indx_g, y_arr_g, y_rind_g,
uni_y_rind_g, y_pind_g, uni_y_pind_g, reac_col_g, prod_col_g,
rstoi_flat_g, pstoi_flat_g, rr_arr_g, rr_arr_p_g, rowvals, colptrs,
jac_wall_indx, jac_part_indx, jac_extr_indx, comp_num, RO2_indx,
RO_indx, HOMRO2_indx, comp_list, Pybel_objects, eqn_num,
comp_namelist, Jlen, rindx_aq, rstoi_aq, pindx_aq, pstoi_aq,
reac_coef_aq, nreac_aq, nprod_aq, jac_stoi_aq, jac_den_indx_aq,
njac_aq, jac_indx_aq, y_arr_aq, y_rind_aq, uni_y_rind_aq,
y_pind_aq, uni_y_pind_aq, reac_col_aq, prod_col_aq, rstoi_flat_aq,
pstoi_flat_aq, rr_arr_aq, rr_arr_p_aq, comp_name, comp_smil, erf,
err_mess, con_C_indx)