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)