def plot_raw():
fld_prj = find_fld_prj(mech)
d = "0.142"
case = "U69_d" + d + "cm"
fld_raw = os.path.join(fld_prj, "detailed", "raw", "[syngas] + [air]",
"DNS", "phi1.0_1.0atm_500.0K", case)
path_npz = os.path.join(fld_raw, "raw.npz")
raw = load_raw(path_npz)
#plt.plot(raw["axis0"], raw["temperature"])
plt.plot(raw["axis0"], raw["mole_fraction"][:, 0])
plt.show()
def run_GPSA(parent, progress):
if not run_graph(parent, progress, 'GPSA'):
return False
min_dT = parent.min_dT
dir_public = parent.project['dir_public']
soln = parent.soln['detailed']
list_train = []
train_name = parent.train_name
for db_name in parent.project['database'].keys():
if parent.project['database'][db_name]['train']:
list_train.append(db_name)
list_GPS = []
for GPS_name in parent.project['GPS'].keys():
if parent.project['GPS'][GPS_name]['checked']:
list_GPS.append(GPS_name)
if bool(list_GPS):
# for different GPS settings ============================
# add new GP
print('run_GPSA: here0')
for GPS_name in list_GPS:
GPS = parent.project['GPS'][GPS_name]
alpha_list = GPS['alpha']
beta_list = GPS['beta']
K_list = GPS['K']
es_name = GPS['es']
es = parent.project['es'][es_name]
traced_list = []
for e in es['element'].keys():
if es['element'][e]['traced']:
traced_list.append(e)
if GPS['iso_enable']:
iso_name = GPS['iso']
iso = parent.project['iso'][iso_name]
gamma_list = GPS['gamma']
else:
iso_name = None
iso = None
gamma_list = [None]
n_GP = 0
for K in K_list:
for beta in beta_list:
for alpha in alpha_list:
for gamma in gamma_list:
dir_sk = para2dir_GPS(dir_public, train_name, \
alpha=alpha, K=K, beta=beta, \
es_name=es_name, iso_name=iso_name, \
d=parent.n_digit, gamma=gamma)
dir_how = os.path.join(dir_sk, 'how')
print('[GPSA] checking dir_how: ' + str(dir_how))
if not os.path.exists(dir_how):
continue
for fo in os.listdir(dir_how):
dir_fo = os.path.join(dir_how, fo)
if ('+' not in fo) or (
not os.path.isdir(dir_fo)):
continue
for reactor in os.listdir(dir_fo):
dir_reactor = os.path.join(dir_fo, reactor)
if (not os.path.isdir(dir_reactor)):
continue
for fat in os.listdir(dir_reactor):
dir_fat = os.path.join(
dir_reactor, fat)
if ('phi' not in fat) or (
not os.path.isdir(dir_fat)):
continue
if reactor == 'DNS':
dir_fat = dir_fat + '/' + os.listdir(
dir_fat)[0]
print('[GPSA] checking dir_fat: ' +
str(dir_fat))
for file in os.listdir(dir_fat):
if 'graph' not in file: continue
file_GP = os.path.join(
dir_fat, file)
traced = file.split(
',')[1].replace(
'graph',
'').strip().upper()
GP_traced = 'GP_' + traced
if GP_traced not in parent.project.keys(
):
parent.project[
GP_traced] = dict()
GPS_results = json.load(
open(file_GP, 'r'))
for GP_name in GPS_results[
'global_path'].keys():
if GP_name not in parent.project[
GP_traced].keys():
GP_dict = dict()
GP_dict['alias'] = GP_name
GP_dict['name'] = GP_name
GP_dict[
'member'] = GPS_results[
'global_path'][
GP_name][
'member']
GP_dict['traced'] = traced
parent.project[GP_traced][
GP_name] = GP_dict
print(
'added ' + traced +
'-traced global pathway: '
+ str(GP_name))
print('run_GPSA: here1')
# find all GP ==============================
GP_list = []
filter_traced = str(parent.w.cb_GPSA_traced.currentText())
print('filter_traced = ' + str(filter_traced))
if filter_traced == 'no filter':
ee = parent.soln['detailed'].element_names
else:
ee = [filter_traced]
alias_only = (str(
parent.w.cb_GPSA_alias.currentText()) == 'with alias only')
source_str = str(parent.w.cb_GPSA_source.currentText())
if source_str == 'no filter':
sources = parent.soln['detailed'].species_names
else:
sources = [source_str]
for traced in ee:
traced = traced.upper()
if 'GP_' + traced in parent.project.keys():
for GP_name in parent.project['GP_' + traced].keys():
GP_dir = parent.project['GP_' + traced][GP_name]
if GP_dir['member'][0] not in sources:
continue
if (not alias_only) or (alias_only and
(GP_dir['alias'] != GP_name)):
GP_list.append((traced, GP_name))
if not bool(GP_list):
msg = 'GP_list is empty!\nTry to run GPS first or loose GPSA settings'
QMessageBox.information(QWidget(), '', msg)
return False
print('len(GP_list) = ' + str(len(GP_list)))
# for different training set ============================
# to compute GPSA quantities
dir_desk = parent.project['mech']['detailed']['desk']
path_R_npz = os.path.join(dir_desk, 'mech', 'radical.npz')
dnR = load_dR(path_R_npz, soln)
soln = parent.soln['detailed']
v = 0.0
dv_db = 100.0 / len(list_train)
for db_name in list_train:
database = parent.project['database'][db_name]
phi_list = database['phi']
T0_list = database['T0']
atm_list = database['atm']
fuel_list = database['fuel']
oxid_list = database['oxid']
reactor = database['reactor']
dv_raw = 1.0 * dv_db / (len(phi_list) * len(atm_list) * len(T0_list) *
len(fuel_list) * len(oxid_list))
dv_GP = 1.0 * dv_raw / len(GP_list)
for fuel_name in fuel_list:
for oxid_name in oxid_list:
for phi in phi_list:
for atm in atm_list:
for T0 in T0_list:
if progress.stop:
progress.close()
return False
fuel = parent.project['fuel'][fuel_name]
oxid = parent.project['oxid'][oxid_name]
fuel_comp = parent.project['fuel'][fuel_name][
'composition']
dir_de = os.path.join(dir_public, 'detailed')
dir_raw = cond2dir(dir_de, fuel_name, \
oxid_name, phi, atm, T0, \
reactor, parent.n_digit)
if 'DNS' in reactor:
dir_raw = os.path.join(dir_raw,
database['case'][0])
raw = load_raw(os.path.join(
dir_raw, 'raw.npz'))
n_break = len(raw['axis0'])
else:
n_break = 0
dir_graph = os.path.join(dir_raw, 'graph')
no_graph = True
if os.path.exists(dir_graph):
for file in os.listdir(dir_graph):
if file.endswith('.json'):
no_graph = False
break
if no_graph:
msg = 'no graph file found for: \n\n' + str(
dir_raw.replace(dir_public,
'[working dir]'))
QMessageBox.information(QWidget(), '', msg)
return False
progress.set_info(str(dir_raw))
for traced, GP_name in GP_list:
msg = ' ' * 4 + 'computing GPSA for ' + str(
GP_name)
print(msg)
progress.set_info(msg)
GP_dir = parent.project['GP_' +
traced][GP_name]
find_GPSA(dir_raw, GP_dir, soln, dnR,
fuel_comp, n_break)
v += dv_GP
progress.set_value('GPSA', v)
return True
def run_GPS(parent, progress):
if not run_graph(parent, progress, 'GPS'):
return False
min_dT = parent.min_dT
dir_public = parent.project['dir_public']
soln = parent.soln['detailed']
list_train = []
train_name = parent.train_name
for db_name in parent.project['database'].keys():
if parent.project['database'][db_name]['train']:
list_train.append(db_name)
list_GPS = []
for GPS_name in parent.project['GPS'].keys():
if parent.project['GPS'][GPS_name]['checked']:
list_GPS.append(GPS_name)
v = 0
if bool(list_GPS) == False:
return False
dv_GPS = 100.0 / len(list_GPS)
# for different GPS settings ============================
for GPS_name in list_GPS:
GPS = parent.project['GPS'][GPS_name]
alpha_list = GPS['alpha']
beta_list = GPS['beta']
K_list = GPS['K']
must_keep = GPS['must_keep']
es_name = GPS['es']
es = parent.project['es'][es_name]
traced_list = []
for e in es['element'].keys():
if es['element'][e]['traced']:
traced_list.append(e)
if GPS['iso_enable']:
iso_name = GPS['iso']
iso = parent.project['iso'][iso_name]
gamma_list = GPS['gamma']
else:
iso_name = None
iso = None
gamma_list = [None]
dv_kab = 1.0 * dv_GPS / (len(K_list) * len(beta_list) *
len(alpha_list) * len(gamma_list))
for K in K_list:
for beta in beta_list:
for alpha in alpha_list:
for gamma in gamma_list:
dir_sk = para2dir_GPS(dir_public, train_name, \
alpha=alpha, K=K, beta=beta, \
es_name=es_name, iso_name=iso_name, \
d=parent.n_digit, gamma=gamma)
progress.set_info('\n' + '-' * 10 + dir_sk + ' ' +
'-' * 10)
dir_mech_sk = os.path.join(dir_sk, 'mech')
path_cti_sk = os.path.join(dir_mech_sk, 'chem.cti')
if os.path.exists(path_cti_sk):
progress.set_info('<already exists, skipped> ' +
path_cti_sk)
v += dv_kab
progress.set_value('GPS', v)
continue
dir_de = os.path.join(dir_public, 'detailed')
dir_mech_de = os.path.join(dir_de, 'mech')
path_cti_de = os.path.join(dir_mech_de, 'chem.cti')
species_kept = set(must_keep)
notes = ['! generated by global pathway selection, Gao et al,'+\
' Combustion and flame, 167 (2016) 238-247']
notes.append('! alpha = ' + str(alpha) + ', K = ' + str(K) + \
', beta = ' + str(beta))
notes.append('! training database: ' + train_name)
# for different training database ============================
dv_db = 1.0 * dv_kab / len(list_train)
for db_name in list_train:
database = parent.project['database'][db_name]
phi_list = database['phi']
T0_list = database['T0']
atm_list = database['atm']
fuel_list = database['fuel']
oxid_list = database['oxid']
reactor = database['reactor']
dv_raw = 1.0 * dv_db / (len(phi_list) * len(atm_list) * len(T0_list) *\
len(fuel_list) * len(oxid_list))
for fuel_name in fuel_list:
for oxid_name in oxid_list:
for phi in phi_list:
for atm in atm_list:
for T0 in T0_list:
if progress.stop:
progress.close()
return False
fuel = parent.project['fuel'][
fuel_name]
oxid = parent.project['oxid'][
oxid_name]
species_kept |= set(
fuel['composition'].keys())
species_kept |= set(
oxid['composition'].keys())
e_available = set()
for sp in fuel[
'composition'].keys():
e_available |= set(
soln.species(sp).
composition.keys())
for sp in oxid[
'composition'].keys():
e_available |= set(
soln.species(sp).
composition.keys())
dir_raw = cond2dir(dir_de, fuel_name, \
oxid_name, phi, atm, T0, \
reactor, parent.n_digit)
if 'DNS' in reactor:
dir_raw = os.path.join(
dir_raw,
database['case'][0])
progress.set_info('raw = '+\
dir_raw.replace(os.path.join(dir_de,'raw'),'').strip('/'))
dir_graph = os.path.join(
dir_raw, 'graph')
#raw_name = dir_raw.replace(\
# os.path.join(dir_de,'raw'),'').strip('/')
raw_name = cond2dir('', fuel_name, \
oxid_name, phi, atm, T0, \
reactor, parent.n_digit)
if 'DNS' in reactor:
raw_name += '/' + database[
'case'][0]
dir_how = os.path.join(
dir_sk,
raw_name.replace(
'raw', 'how'))
if not os.path.exists(dir_how):
os.makedirs(dir_how)
raw = load_raw(
os.path.join(
dir_raw, 'raw.npz'))
T = raw['temperature']
axis0 = raw['axis0']
# for different time instance ================
flag = False
# -----------------------------------------------
# I only consider the points where T and T0 has
# some difference, which means there're reactions
# performing GPS on chemically frozen state, or
# equilibirum state (for PSR), does not give too
# much useful information
#
# once a point is sampled, flag = True
# -----------------------------------------------
dv_pnt = 1.0 * dv_raw / len(T)
for i_pnt in range(len(T)):
"""
if 'active reactions' in raw.keys():
if raw['active reactions'][i_pnt] == 0:
print 'skipped pnt '+str(i_pnt)+' as no active reaction'
continue
"""
if flag == False:
if abs(T[i_pnt] -
T[0]) > min_dT:
flag = True
# for different source->target ==============
for e in traced_list:
if e not in e_available:
continue
sources = copy.copy(
es['element'][e]
['source'])
if bool(sources
) == False:
sources = [None]
if parent.alias_fuel in sources:
del sources[
sources.index(
parent.
alias_fuel
)]
for sp in fuel[
'composition'].keys(
):
atoms = soln.species(
sp
).composition.keys(
)
#print 'atms of ' + sp + ' = ' +str(atoms)
if e in atoms:
sources += [
sp
]
targets = es[
'element'][e][
'target']
if bool(targets
) == False:
targets = [None]
for target in targets:
for source in sources:
name_how = st2name(
i_pnt, e,
source,
target)
if progress.verbose:
progress.set_info(
' ' *
5 +
name_how
)
path_gps = os.path.join(
dir_how,
name_how +
'.json')
path_graph = os.path.join(
dir_graph,
e + '_' +
str(i_pnt)
+ '.json')
if os.path.exists(
path_graph
):
data = json.load(\
open(path_graph, 'r'))
flux_graph = json_graph.node_link_graph(
data)
else:
if progress.verbose:
progress.set_info(
' '
*
10
+
'building graph...'
)
dir_graph = os.path.join(
dir_raw,
'graph'
)
if not os.path.exists(
dir_graph
):
os.makedirs(
dir_graph
)
flux_graph = build_flux_graph(soln, raw, e, \
path_save=path_graph, overwrite=False, \
i0=i_pnt, i1=i_pnt, constV=False)
if flag == False:
continue
GPS_notes = 'T = '+str(T[i_pnt])+', axis0 = '+str(axis0[i_pnt])+\
' ('+str(min(axis0))+' ~ '+str(max(axis0))+')'
GPS_results = GPS_algo(soln, flux_graph, source, target, \
path_save=path_gps, K=K, alpha=alpha, beta=beta, \
normal='max', iso=iso, overwrite=True, raw=dir_raw, \
notes=GPS_notes, gamma=gamma)
new_kept = set(
GPS_results[
'species']
.keys())
species_kept |= new_kept
v += dv_pnt
progress.set_value(
'GPS', v)
# generate chem.inp ***************
write_sk_inp(species_kept, dir_mech_de, dir_mech_sk,
notes)
#"""
progress.set_value('GPS', 100)
return True
def run_graph(parent, progress, task):
if task == 'GPS':
obj = progress.w.label_GPS
elif task == 'GPSA':
obj = progress.w.label_GPSA
obj.setText('building graph')
dir_public = parent.project['dir_public']
soln = parent.soln['detailed']
list_train = []
train_name = parent.train_name
for db_name in parent.project['database'].keys():
if parent.project['database'][db_name]['train']:
list_train.append(db_name)
traced_list = []
for GPS_name in parent.project['GPS'].keys():
if parent.project['GPS'][GPS_name]['checked']:
GPS = parent.project['GPS'][GPS_name]
es_name = GPS['es']
es = parent.project['es'][es_name]
for e in es['element'].keys():
if es['element'][e]['traced']:
if e not in traced_list:
traced_list.append(e)
if not bool(traced_list):
msg = 'no traced element in selected GPS'
QMessageBox.information(QWidget(), '', msg)
return False
v = 0.0
dv_db = 100.0 / len(list_train)
for db_name in list_train:
database = parent.project['database'][db_name]
phi_list = database['phi']
T0_list = database['T0']
atm_list = database['atm']
fuel_list = database['fuel']
oxid_list = database['oxid']
reactor = database['reactor']
dv_raw = dv_db / (len(phi_list) * len(atm_list) * len(T0_list) *\
len(fuel_list) * len(oxid_list))
for fuel_name in fuel_list:
for oxid_name in oxid_list:
for phi in phi_list:
for atm in atm_list:
for T0 in T0_list:
if progress.stop:
progress.close()
return False
dir_de = os.path.join(dir_public, 'detailed')
dir_raw = cond2dir(dir_de, fuel_name, \
oxid_name, phi, atm, T0, \
reactor, parent.n_digit)
if 'DNS' in reactor:
dir_raw = os.path.join(dir_raw,
database['case'][0])
raw = load_raw(os.path.join(dir_raw, 'raw.npz'))
dir_graph = os.path.join(dir_raw, 'graph')
if not os.path.exists(dir_graph):
os.makedirs(dir_graph)
n_pnt = len(raw['axis0'])
dv_pnt = 1.0 * dv_raw / n_pnt
print('dir_raw = ' + str(dir_raw))
print('n_point = ' + str(n_pnt))
for i_pnt in range(n_pnt):
"""
if 'active reactions' in raw.keys() and len(raw['active reactions'])>0:
if raw['active reactions'][i_pnt] == 0:
print 'skipped pnt '+str(i_pnt)+' as no active reaction'
continue
"""
for e in traced_list:
path_graph = os.path.join(
dir_graph,
e + '_' + str(i_pnt) + '.json')
if not os.path.exists(path_graph):
info = 'building '+e+'-graph for pnt'+str(i_pnt)+' of '+\
str(dir_raw.replace(dir_de,''))
if i_pnt % 10 == 0:
print(info)
if n_pnt < 100:
progress.set_info(info)
flux_graph = build_flux_graph(soln, raw, e, \
path_save=path_graph, overwrite=False, \
i0=i_pnt, i1=i_pnt, constV=False)
else:
if i_pnt % 1e4 == 0 or i_pnt == n_pnt - 1:
print('already exists ' +
str(path_graph))
v += dv_pnt
if n_pnt < 100:
progress.set_value(task, v)
obj.setText(task)
progress.set_value(task, 0.0)
return True
def find_yy(soln, dir_raw, parent, fig_opt, sub_opt, tp):
# tp is type
"""
.8888b oo dP
88 " 88
88aaa dP 88d888b. .d888b88 dP dP dP dP
88 88 88' `88 88' `88 88 88 88 88
88 88 88 88 88. .88 88. .88 88. .88
dP dP dP dP `88888P8 `8888P88 `8888P88
oooooooooooo .88 .88
d8888P d8888P
"""
#dnR = load_dR(path_R_npz, soln)
path_raw = os.path.join(dir_raw, 'raw.npz')
raw = load_raw(path_raw)
xtype = fig_opt['xtype']
mf = raw['mole_fraction']
mole = [float(v) for v in raw['mole']]
xx = [float(v) for v in raw['axis0']]
TT = [float(v) for v in raw['temperature']]
# ==========================================
if '_T' in tp:
if xtype == 'Temperature (K)':
yy = [xx]
else:
yy = [TT]
ff = ['']
elif '_Qdot' in tp:
yy = [raw['heat_release_rate']]
ff = ['']
# ==========================================
elif '_tau-ign' in tp:
yy = [xx]
ff = ['']
# ==========================================
elif '_psr-T' in tp:
yy = [TT]
ff = ['']
# ==========================================
elif '_sp' in tp:
yy = []
ff = []
for i_sp in range(len(sub_opt['sp'])):
sp = sub_opt['sp'][i_sp]
yy.append([])
ff.append(sp)
for i_pnt in range(len(raw['axis0'])):
soln = raw2soln(soln, raw, i_pnt)
for i_sp in range(len(sub_opt['sp'])):
sp = sub_opt['sp'][i_sp]
if sp != 'radical':
sp_id_list = [soln.species_index(sp)]
else:
sp_id_list = [
soln.species_index(R) for R in ['O', 'H', 'OH']
]
yi = 0
for sp_id in sp_id_list:
if sub_opt['task'] == 'mole fraction':
yi += float(mf[i_pnt, sp_id])
else:
yi += soln.net_production_rates[sp_id]
yy[i_sp].append(yi)
# ==========================================
elif '_GP' in tp:
key = 'GP_' + sub_opt['traced']
method = sub_opt['method']
traced = sub_opt['traced']
yy = []
ff = []
for i_GP in range(len(sub_opt[key])):
GP_name = sub_opt[key][i_GP]
GP_dir = parent.project[key][GP_name]
GP_alias = GP_dir['alias']
y = load_GPSA(dir_raw, GP_dir, method)
if y is None:
msg = 'could not find GPSA data for: \n'+GP_alias+' \nin:\n '+str(dir_raw)[-20:]+\
'try to run GPSA first'
QMessageBox.information(QWidget(), '', msg)
return False, False, False, False
yy.append(y)
ff.append(GP_alias)
# ==========================================
elif '_node' in tp:
extra = {
'n_edge': int(sub_opt['n_edge'][0]),
'traced': sub_opt['traced'],
'species': soln.species_names
}
yy, ff = find_node_edges(dir_raw, sub_opt['node'], extra)
ff_sorted = sorted(ff)
yy_sorted = []
for f in ff_sorted:
i_f = ff.index(f)
yy_sorted.append(yy[i_f])
# ff is the label
return yy_sorted, xx, TT, ff_sorted
def find_GPSA(dir_raw, GP_dict, soln, dnR, fuel_comp, n_break=0):
GP_name = GP_dict['name']
traced = GP_dict['traced']
dir_save = os.path.join(dir_raw,'GPSA',traced)
if not os.path.exists(dir_save):
os.makedirs(dir_save)
path_save = os.path.join(dir_save, shorten_GP_name(GP_name)+'.json')
# =====================================
# if previously computed, return False
GPSA_all = dict()
if os.path.exists(path_save):
GPSA_all = json.load(open(path_save,'r'))
if GP_name in GPSA_all.keys():
return False
# =====================================
# if not loaded, compute these results
print 'computing GPSA for '+GP_name
traced = GP_dict['traced']
GP_member = GP_dict['member']
dir_graph = os.path.join(dir_raw,'graph')
path_raw = os.path.join(dir_raw,'raw.npz')
raw = load_raw(path_raw)
rr_mat = raw['net_reaction_rate']
GPSA = dict()
GPSA['R_GP'] = [] # net radical production rate associated with a Global Pathway (GP)
GPSA['Q_GP'] = [] # net heat release rate associated with a GP
GPSA['D_GP'] = [] # dominancy of a GP
GPSA['R_ij'] = dict() # net radical production rate associated with a conversion step (from the i-th species to the j-th species)
GPSA['Q_ij'] = dict()
GPSA['a_iji'] = dict()
#GPSA['perc_ij'] = dict()
for i in range(len(GP_member)-1):
edge = find_edge_name(GP_member, i)
GPSA['R_ij'][edge] = dict()
GPSA['R_ij'][edge]['member'] = []
GPSA['R_ij'][edge]['net'] = []
GPSA['Q_ij'][edge] = dict()
GPSA['Q_ij'][edge]['member'] = []
GPSA['Q_ij'][edge]['net'] = []
GPSA['a_iji'][edge] = dict()
GPSA['a_iji'][edge]['member'] = []
GPSA['a_iji'][edge]['net'] = []
#GPSA['perc_ij'][edge] = dict()
#GPSA['perc_ij'][edge]['member'] = []
#GPSA['perc_ij'][edge]['net'] = []
source = GP_dict['member'][0]
traced = GP_dict['traced']
if source not in fuel_comp.keys():
perc_from_source = 0.0
else:
total_atom = 0
for k in fuel_comp.keys():
sp = soln.species(k)
atom = 0.0
if traced in sp.composition.keys():
atom += fuel_comp[k] * sp.composition[traced]
if source == k:
atom_source = atom
total_atom += atom
perc_from_source = 1.0 * atom_source / total_atom
#print 'total '+traced+' atoms for '+str(fuel_comp)+' is '+str(total_atom)
#print 'source '+str(source)+' has '+str(atom_source)+' atms'
#print 'so perc_from_source = '+str(perc_from_source)
#GPSA['perc_ij']['from_source'] = perc_from_source
# for each point -----------
i_pnt = 0
while True:
path_graph = os.path.join(dir_graph, traced+'_'+str(i_pnt) + '.json')
if not os.path.exists(path_graph):
if i_pnt>n_break:
print 'break as cannot find: '+str(path_graph)
break
else:
# fill this with None ---------------
if i_pnt%10 == 0:
print ' fill None GPSA for '+str(path_graph)
for i in range(len(GP_member)-1):
s = GP_member[i]
t = GP_member[i+1]
edge = find_edge_name(GP_member, i)
for k in ['member','net']:
GPSA['R_ij'][edge][k].append(None)
GPSA['Q_ij'][edge][k].append(None)
GPSA['a_iji'][edge][k].append(None)
#GPSA['perc_ij'][edge][k].append(None)
GPSA['R_GP'].append(None)
GPSA['D_GP'].append(None)
i_pnt += 1
continue
soln = raw2soln(soln, raw, i_pnt)
if i_pnt%10 == 0:
print ' finding GPSA for '+str(path_graph)
# fill this with real value ---------------
#norm_Rpro = 0.0
#norm_Rcon = 0.0
for id_rxn in range(soln.n_reactions):
dR = dnR[id_rxn] * rr_mat[i_pnt, id_rxn]
#norm_Rpro += max(0, dR)
#norm_Rcon += max(0, -dR)
flux_graph = json_graph.node_link_graph(json.load(open(path_graph, 'r')))
out_deg = flux_graph.out_degree(weight='flux')
norm_out_deg = sum([out_deg[m] for m in fuel_comp.keys() if m in out_deg.keys()])
flux = []
rxn_involved = []
sum_OMEGA_R = 0
sum_OMEGA_Q = 0
perc_ij_list = []
# for each edge (conversion step) -----------------
for i in range(len(GP_member)-1):
s = GP_member[i]
t = GP_member[i+1]
edge = find_edge_name(GP_member, i)
GPSA['R_ij'][edge]['member'].append(dict())
GPSA['Q_ij'][edge]['member'].append(dict())
GPSA['a_iji'][edge]['member'].append(dict())
#GPSA['perc_ij'][edge]['member'].append(dict())
# ------------------------------
try:
st = flux_graph[s][t]
except KeyError:
st = None
perc_ij = None
if st is not None:
flux.append(st['flux'])
perc_ij = 1.0 * st['flux'] / out_deg[s]
perc_ij_list.append(perc_ij)
for id_rxn_s in st['member'].keys():
id_rxn = int(id_rxn_s)
rxn = soln.reaction_equation(id_rxn)
rr = rr_mat[i_pnt, id_rxn]
if rr < 0:
sign_rxn = -id_rxn
else:
sign_rxn = id_rxn
GPSA['a_iji'][edge]['member'][i_pnt][sign_rxn] = st['member'][id_rxn_s]
#GPSA['perc_ij'][edge]['member'][i_pnt][sign_rxn] = 1.0 * st['member'][id_rxn_s]/out_deg[s]
OMEGA_R = float(rr * dnR[id_rxn])
GPSA['R_ij'][edge]['member'][i_pnt][sign_rxn] = OMEGA_R
OMEGA_Q = float(rr * soln.delta_enthalpy[id_rxn])
GPSA['Q_ij'][edge]['member'][i_pnt][sign_rxn] = OMEGA_Q
if id_rxn not in rxn_involved:
sum_OMEGA_R += OMEGA_R
sum_OMEGA_Q += OMEGA_Q
rxn_involved.append(id_rxn)
# ------------------------------
try:
ts = flux_graph[t][s]
except KeyError:
ts = None
if ts is not None:
for id_rxn_s in ts['member'].keys():
id_rxn = int(id_rxn_s)
rxn = soln.reaction_equation(id_rxn)
rr = rr_mat[i_pnt, id_rxn]
if rr < 0:
sign_rxn = -id_rxn
else:
sign_rxn = id_rxn
GPSA['a_iji'][edge]['member'][i_pnt][sign_rxn] = - ts['member'][id_rxn_s]
# ------------------------------
GPSA['R_ij'][edge]['net'].append(sum(GPSA['R_ij'][edge]['member'][i_pnt].values()))
GPSA['Q_ij'][edge]['net'].append(sum(GPSA['Q_ij'][edge]['member'][i_pnt].values()))
GPSA['a_iji'][edge]['net'].append(sum(GPSA['a_iji'][edge]['member'][i_pnt].values()))
#GPSA['perc_ij'][edge]['net'].append(perc_ij)
domi_perc = gmean(perc_ij_list)*perc_from_source
if bool(flux):
min_flux = min(flux)
if norm_out_deg>0:
domi_flux = 1.0 * min_flux/norm_out_deg
else:
domi_flux = float('nan')
else:
min_flux = 0.0
domi_flux = 0.0
R_GP = domi_perc * sum_OMEGA_R
Q_GP = domi_perc * sum_OMEGA_Q
GPSA['R_GP'].append(R_GP)
GPSA['Q_GP'].append(Q_GP)
GPSA['D_GP'].append(domi_perc)
i_pnt += 1
GPSA_all[GP_name] = GPSA
json.dump(GPSA_all, open(path_save,'w'))
return True
def find_GP_order(dir_raw, traced, parent, sample, method='D_GP'):
path_raw = os.path.join(dir_raw, 'raw.npz')
raw = load_raw(path_raw)
if sample['by'] != 'max':
i_plot = find_i_plot(sample['at'], raw, sample_by=sample['by'])
GP_traced = parent.project['GP_' + traced]
list_GP_name = []
list_GP_source = []
list_GP_target = []
list_GP_cc = []
list_GP_nan = []
any_available = False
for GP_name in GP_traced.keys():
GP_dir = GP_traced[GP_name]
GP_alias = GP_dir['alias']
member = GP_dir['member']
cc = load_GPSA(dir_raw, GP_dir, method)
if cc is None:
c = 0
list_GP_nan.append(True)
else:
any_available = True
if sample['by'] == 'max':
c = max(cc)
else:
c = cc[i_plot]
list_GP_nan.append(False)
list_GP_name.append(GP_name)
list_GP_source.append(member[0])
list_GP_target.append(member[-1])
list_GP_cc.append(c)
try:
# sort by source first, then target, then cc
ind = np.lexsort((list_GP_cc, list_GP_target, list_GP_source))
except ValueError:
print(list_GP_cc)
print(list_GP_target)
print(list_GP_source)
import sys
sys.exit()
#print 'lexsort OK'
if not any_available:
msg = 'no '+traced+'-GPSA data is available for\n\n'+str(dir_raw)+\
'\n\ntry different dataset or run GPSA first'
QMessageBox.information(QWidget(), '', msg)
list_GP_name_sorted = [list_GP_name[i] for i in ind]
list_GP_nan_sorted = [list_GP_nan[i] for i in ind]
if bool(dir_raw):
if max(list_GP_cc) > 0:
norm = max(list_GP_cc)
else:
norm = 1.0
list_GP_cc_norm_sorted = [list_GP_cc[i] / norm for i in ind]
else:
list_GP_cc_norm_sorted = list_GP_cc
return list_GP_name_sorted, list_GP_cc_norm_sorted, list_GP_nan_sorted