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@ -1,4 +1,4 @@
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import time
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from datetime import datetime
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import cantera as ct
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import cantera as ct
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import pandas as pd
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import pandas as pd
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import numpy as np
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import numpy as np
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@ -7,7 +7,8 @@ from scipy.optimize import minimize
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import xml.etree.ElementTree as ET
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import xml.etree.ElementTree as ET
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import seaborn as sns
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import seaborn as sns
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import matplotlib.pyplot as plt
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import matplotlib.pyplot as plt
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import shutil
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import copy
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sns.set()
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sns.set()
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@ -17,8 +18,7 @@ class REEPS:
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Returns parameters for GEM
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Returns parameters for GEM
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:param exp_csv_filename: (str) csv file name with experimental data
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:param exp_csv_filename: (str) csv file name with experimental data
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:param phases_xml_filename: (str) xml file with parameters for equilibrium calc
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:param phases_xml_filename: (str) xml file with parameters for equilibrium calc
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:param x_guess: (float) guess for multiplier variable
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:param opt_dict: (dict) optimize info {species:{thermo_prop:guess}
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:param h_guess: (float) initial guess standard enthalpy (J/kmol)
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:param phase_names: (list) names of phases in xml file
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:param phase_names: (list) names of phases in xml file
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:param aq_solvent_name: (str) name of aqueous solvent in xml file
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:param aq_solvent_name: (str) name of aqueous solvent in xml file
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:param extractant_name: (str) name of extractant in xml file
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:param extractant_name: (str) name of extractant in xml file
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@ -34,8 +34,7 @@ class REEPS:
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def __init__(self,
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def __init__(self,
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exp_csv_filename,
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exp_csv_filename,
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phases_xml_filename,
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phases_xml_filename,
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x_guess,
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opt_dict,
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h_guess,
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phase_names,
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phase_names,
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aq_solvent_name,
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aq_solvent_name,
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extractant_name,
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extractant_name,
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@ -48,8 +47,7 @@ class REEPS:
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):
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):
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self._exp_csv_filename = exp_csv_filename
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self._exp_csv_filename = exp_csv_filename
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self._phases_xml_filename = phases_xml_filename
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self._phases_xml_filename = phases_xml_filename
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self._x_guess = x_guess
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self._opt_dict = opt_dict
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self._h_guess = h_guess
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self._phase_names = phase_names
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self._phase_names = phase_names
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self._aq_solvent_name = aq_solvent_name
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self._aq_solvent_name = aq_solvent_name
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self._extractant_name = extractant_name
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self._extractant_name = extractant_name
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@ -60,6 +58,8 @@ class REEPS:
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self._extractant_rho = extractant_rho
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self._extractant_rho = extractant_rho
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self._diluant_rho = diluant_rho
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self._diluant_rho = diluant_rho
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self._temp_xml_filename = "temp.xml"
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shutil.copyfile(phases_xml_filename, self._temp_xml_filename)
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self._phases = ct.import_phases(phases_xml_filename, phase_names)
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self._phases = ct.import_phases(phases_xml_filename, phase_names)
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self._exp_df = pd.read_csv(self._exp_csv_filename)
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self._exp_df = pd.read_csv(self._exp_csv_filename)
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@ -90,18 +90,11 @@ class REEPS:
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self.set_in_moles(feed_vol=1)
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self.set_in_moles(feed_vol=1)
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return None
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return None
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def get_x_guess(self) -> float:
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def get_opt_dict(self) -> dict:
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return self._x_guess
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return self._opt_dict
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def set_x_guess(self, x_guess):
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self._x_guess = x_guess
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return None
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def get_h_guess(self) -> float:
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return self._h_guess
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def set_h_guess(self, h_guess):
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def set_opt_dict(self, opt_dict):
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self._h_guess = h_guess
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self._opt_dict = opt_dict
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return None
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return None
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def get_aq_solvent_name(self) -> str:
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def get_aq_solvent_name(self) -> str:
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@ -161,7 +154,8 @@ class REEPS:
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return None
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return None
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def set_in_moles(self, feed_vol):
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def set_in_moles(self, feed_vol):
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""":param feed_vol: (float) feed volume of mixture (g/L)"""
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"""Function that initializes mole fractions
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:param feed_vol: (float) feed volume of mixture (g/L)"""
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phases_copy = self._phases.copy()
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phases_copy = self._phases.copy()
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exp_df = self._exp_df.copy()
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exp_df = self._exp_df.copy()
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solvent_name = self._aq_solvent_name
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solvent_name = self._aq_solvent_name
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@ -244,8 +238,10 @@ class REEPS:
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return self._in_moles
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return self._in_moles
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def objective(self, x):
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def objective(self, x):
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h = x[0] * self._h_guess
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"""Log mean squared error between measured and predicted data
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phases_copy = self._phases.copy()
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:param x: (list) thermo properties varied to minimize LMSE"""
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temp_xml_filename = self._temp_xml_filename
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phase_names = self._phase_names
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aq_ind = self._aq_ind
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aq_ind = self._aq_ind
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org_ind = self._org_ind
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org_ind = self._org_ind
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complex_name = self._complex_name
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complex_name = self._complex_name
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@ -253,18 +249,16 @@ class REEPS:
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in_moles = self._in_moles
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in_moles = self._in_moles
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exp_df = self._exp_df
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exp_df = self._exp_df
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complex_index = phases_copy[org_ind].species_index(complex_name)
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x = np.array(x)
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complex_species = phases_copy[org_ind].species(complex_index)
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opt_dict = copy.deepcopy(self._opt_dict)
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i = 0
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new_thermo_coeffs = complex_species.thermo.coeffs
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for species_name in opt_dict.keys():
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new_thermo_coeffs[1] = h
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for thermo_prop in opt_dict[species_name].keys():
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complex_species.thermo = ct.ConstantCp(
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opt_dict[species_name][thermo_prop] *= x[i]
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complex_species.thermo.min_temp,
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i += 1
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complex_species.thermo.max_temp,
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self.update_xml(opt_dict, temp_xml_filename)
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complex_species.thermo.reference_pressure,
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new_thermo_coeffs)
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phases_copy[org_ind].modify_species(complex_index, complex_species)
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phases_copy = ct.import_phases(temp_xml_filename, phase_names)
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mix = ct.Mixture(phases_copy)
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mix = ct.Mixture(phases_copy)
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pred = []
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pred = []
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for row in in_moles.values:
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for row in in_moles.values:
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@ -285,30 +279,48 @@ class REEPS:
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Returns estimated complex enthalpy in J/mol
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Returns estimated complex enthalpy in J/mol
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:param kwargs: (dict) parameters and options for scipy.minimize
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:param kwargs: (dict) parameters and options for scipy.minimize
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"""
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"""
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x_guess = self._x_guess
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opt_dict = copy.deepcopy(self._opt_dict)
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h_guess = self._h_guess
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# x_guess = []
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i = 0
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for species_name in opt_dict.keys():
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for _ in opt_dict[species_name].keys():
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# x_guess.append(opt_dict[species_name][thermo_prop])
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i += 1
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x_guess = np.ones(i)
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res = minimize(self.objective, x_guess, **kwargs)
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res = minimize(self.objective, x_guess, **kwargs)
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pred_complex_enthalpy = res.x[0] * h_guess / 1000 # J/mol
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i = 0
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return pred_complex_enthalpy
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for species_name in opt_dict.keys():
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for thermo_prop in opt_dict[species_name].keys():
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opt_dict[species_name][thermo_prop] *= res.x[i]
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i += 1
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return opt_dict
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def update_xml(self,
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def update_xml(self,
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complex_enthalpy,
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info_dict,
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phases_xml_filename=None,
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phases_xml_filename=None):
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complex_name=None):
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"""updates xml file with info_dict
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"""updates xml file with new complex_enthalpy"""
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:param info_dict: (dict) info in {species_names:{thermo_prop:val}}
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:param phases_xml_filename: (str) xml filename if editing other xml
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"""
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if phases_xml_filename is None:
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if phases_xml_filename is None:
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phases_xml_filename = self._phases_xml_filename
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phases_xml_filename = self._phases_xml_filename
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if complex_name is None:
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complex_name = self._complex_name
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tree = ET.parse(phases_xml_filename)
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tree = ET.parse(phases_xml_filename)
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root = tree.getroot()
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root = tree.getroot()
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# Update xml file
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# Update xml file
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for species_name in info_dict.keys():
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for thermo_prop in info_dict[species_name].keys():
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for species in root.iter('species'):
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for species in root.iter('species'):
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if species.attrib['name'] is complex_name:
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if species.attrib['name'] == species_name:
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for h0 in species.iter('h0'):
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for changed_prop in species.iter(thermo_prop):
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h0.text = str(complex_enthalpy)
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changed_prop.text = str(
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h0.set('updated', 'Updated at ' + time.strftime('%X'))
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info_dict[species_name][thermo_prop])
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now = datetime.now()
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changed_prop.set('updated',
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'Updated at {0}:{1} {2}-{3}-{4}'
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.format(now.hour, now.minute,
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now.month, now.day,
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now.year))
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tree.write(phases_xml_filename)
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tree.write(phases_xml_filename)
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titusquah
5 years ago