def propane_make_figures(data_dir, species_path=False):
"""
make figures for propane system
"""
g_s = global_settings.get_setting(data_dir)
spe_idx, _, spe_exclude_name = trajectory.get_species_with_top_n_concentration(
data_dir,
exclude=None,
top_n=g_s['top_n_s'],
traj_max_t=g_s['traj_max_t'],
tau=g_s['tau'],
end_t=g_s['end_t'],
tag=g_s['tag'],
atoms=[g_s['atom_f']])
mf.plot_concentrations(data_dir,
spe_idx=spe_idx,
tau=g_s['tau'],
end_t=g_s['end_t'],
tag=g_s['tag'],
exclude_names=spe_exclude_name,
renormalization=True)
mf.plot_reaction_rates(data_dir,
reaction_idx=[1068, 1070, 1072, 1074, 1076],
tau=g_s['tau'],
end_t=1.0,
tag=g_s['tag'])
for s_i in spe_idx:
print(spe_idx)
mf.plot_species_pathway_prob(data_dir,
top_n=g_s['top_n_p'],
exclude_names=spe_exclude_name,
init_spe=g_s['init_s'],
atom_followed=g_s['atom_f'],
tau=g_s['tau'],
end_t=g_s['end_t'],
end_s_idx=s_i,
species_path=species_path)
mf.plot_reaction_rate_constant(data_dir)
mf.plot_top_n_spe_concentration(data_dir,
exclude_names=None,
atom_followed=g_s['atom_f'],
end_t=g_s['end_t'],
top_n=10)
def get_suffix(data_dir,
init_spe=None,
atom_followed=None,
end_t=None,
len_threshold=100):
"""
get suffix
"""
g_s = global_settings.get_setting(data_dir)
suffix = ""
if init_spe is None:
suffix += "_S" + str(g_s['init_s'])
else:
suffix += "_S" + str(init_spe)
if atom_followed is None:
suffix += "_" + str(g_s['atom_f'])
else:
suffix += "_" + str(atom_followed)
if end_t is None:
suffix += "_" + str(g_s['end_t'])
else:
suffix += "_" + str(end_t)
# add mc_n_traj
suffix += "_" + str(int(g_s['mc_n_traj']))
# add pi_n_traj
suffix += "_" + str(int(g_s['pi_n_traj']))
# add top_n_p
suffix += "_" + str(int(g_s['top_n_p']))
# path reg
if len(suffix) < len_threshold and g_s['path_reg'] is not None:
suffix += "_include_" + str(valid_name(g_s['path_reg']))
# no path reg
if len(suffix) < len_threshold and g_s['no_path_reg'] is not None:
suffix += "_exclude_" + str(valid_name(g_s['no_path_reg']))
if len(suffix) > len_threshold:
suffix = suffix[0:len_threshold]
if len(suffix) > 0 and suffix[-1] == '_':
suffix = suffix[0:-1]
return suffix
if indicator is True:
rxn_idx_good.append(int(rxn_idx))
rxn_name_good.append(reaction_info[rxn_idx]['reaction_name'])
if p_reactant != -1:
rxn_principal_reactant.append(p_reactant)
print(rxn_idx_good)
print(rxn_name_good)
print(rxn_principal_reactant)
return rxn_idx_good, rxn_principal_reactant
if __name__ == "__main__":
DATA_DIR = os.path.abspath(
os.path.join(os.path.realpath(sys.argv[0]), os.pardir, os.pardir,
os.pardir, os.pardir, "SOHR_DATA"))
G_S = global_settings.get_setting(DATA_DIR)
# species_count(DATA_DIR)
reaction_count(DATA_DIR, top_n=100, norm=True)
# initiation_reaction_count(DATA_DIR)
# species_cycle(DATA_DIR)
# print(parse_species_production_path("S114R15S9R15S9", 'S9'))
# species_production_path(DATA_DIR, spe='OH', top_n=50)
# print(parse_species_production_reaction("S114R15S9R47S9", 'S9'))
# species_production_reaction(DATA_DIR, spe='OH', top_n=50)
# SPE_LIST = [14, 59, 17, 44, 38, 86, 69, 15, 82]
# for es in SPE_LIST:
# path_length_statistics(
# DATA_DIR, init_spe=G_S['init_s'], atom_followed=G_S['atom_f'], end_t=G_S['end_t'], end_spe=es)
