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@ -1,5 +1,13 @@
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import time
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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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from scipy.optimize import minimize
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# noinspection PyPep8Naming
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import xml.etree.ElementTree as ET
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import seaborn as sns
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import matplotlib.pyplot as plt
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sns.set()
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class REEPS:
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class REEPS:
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@ -7,13 +15,15 @@ class REEPS:
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Takes in experimental data
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Takes in experimental data
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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 param_xml_file: (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 x_guess: (float) guess for multiplier variable
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:param h_guess: (float) initial guess standard enthalpy (J/kmol)
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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
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:param extractant_name: (str) name of extractant in xml file
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:param diluant_name: (str) name of diluant
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:param diluant_name: (str) name of diluant in xml file
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:param complex_name: (str) name of complex in xml file
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:param rare_earth_ion_name: (str) name of rare earth ion in xml file
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:param aq_solvent_rho: (float) density of solvent (g/L)
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:param aq_solvent_rho: (float) density of solvent (g/L)
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:param extractant_rho: (float) density of extractant (g/L)
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:param extractant_rho: (float) density of extractant (g/L)
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:param diluant_rho: (float) density of extractant (g/L)
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:param diluant_rho: (float) density of extractant (g/L)
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@ -22,32 +32,42 @@ 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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param_xml_file,
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phases_xml_filename,
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x_guess,
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x_guess,
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h_guess,
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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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diluant_name,
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diluant_name,
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complex_name,
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rare_earth_ion_name,
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aq_solvent_rho=None,
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aq_solvent_rho=None,
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extractant_rho=None,
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extractant_rho=None,
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diluant_rho=None,
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diluant_rho=None,
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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._x_guess = x_guess
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self._x_guess = x_guess
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self._h_guess = h_guess
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self._h_guess = h_guess
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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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self._diluant_name = diluant_name
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self._diluant_name = diluant_name
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self._complex_name = complex_name
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self._rare_earth_ion_name = rare_earth_ion_name
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self._aq_solvent_rho = aq_solvent_rho
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self._aq_solvent_rho = aq_solvent_rho
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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._phases = ct.import_phases(param_xml_file, 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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self._in_moles = None
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self._in_moles = None
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self.set_in_moles()
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self._aq_ind = None
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self._org_ind = None
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self.set_in_moles(feed_vol=1)
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def get_exp_csv_filename(self) -> str:
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def get_exp_csv_filename(self) -> str:
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return self._exp_csv_filename
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return self._exp_csv_filename
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@ -60,8 +80,13 @@ class REEPS:
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def get_phases(self) -> list:
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def get_phases(self) -> list:
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return self._phases
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return self._phases
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def set_phases(self, param_xml_file, phase_names):
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def set_phases(self, phases_xml_filename, phase_names):
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self._phases = ct.import_phases(param_xml_file, phase_names)
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"""Change xml and phase names
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Also runs set_in_mole to set initial moles to 1 g/L"""
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self._phases_xml_filename = phases_xml_filename
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self._phase_names = phase_names
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self._phases = ct.import_phases(phases_xml_filename, phase_names)
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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_x_guess(self) -> float:
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@ -98,7 +123,21 @@ class REEPS:
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def set_diluant_name(self, diluant_name):
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def set_diluant_name(self, diluant_name):
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self._diluant_name = diluant_name
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self._diluant_name = diluant_name
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return None
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return None
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def get_complex_name(self) -> str:
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return self._complex_name
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def set_complex_name(self, complex_name):
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self._complex_name = complex_name
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return None
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def get_rare_earth_ion_name(self) -> str:
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return self._rare_earth_ion_name
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def set_rare_earth_ion_name(self, rare_earth_ion_name):
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self._rare_earth_ion_name = rare_earth_ion_name
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return None
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def get_aq_solvent_rho(self) -> str:
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def get_aq_solvent_rho(self) -> str:
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return self._aq_solvent_rho
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return self._aq_solvent_rho
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@ -120,7 +159,8 @@ class REEPS:
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self._diluant_rho = diluant_rho
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self._diluant_rho = diluant_rho
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return None
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return None
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def set_in_moles(self):
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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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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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@ -145,6 +185,8 @@ class REEPS:
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org_ind = 1
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org_ind = 1
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else:
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else:
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org_ind = 0
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org_ind = 0
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self._aq_ind = aq_ind
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self._org_ind = org_ind
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extractant_ind = phases_copy[org_ind].species_names.index(
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extractant_ind = phases_copy[org_ind].species_names.index(
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extractant_name)
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extractant_name)
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diluant_ind = phases_copy[org_ind].species_names.index(diluant_name)
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diluant_ind = phases_copy[org_ind].species_names.index(diluant_name)
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@ -156,19 +198,18 @@ class REEPS:
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diluant_mw = mix_org.molecular_weights[diluant_ind]
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diluant_mw = mix_org.molecular_weights[diluant_ind]
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if solvent_rho is None:
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if solvent_rho is None:
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solvent_rho = mix_aq(aq_ind).partial_molar_volumes[
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solvent_rho = mix_aq(aq_ind).partial_molar_volumes[
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solvent_ind]/solvent_mw * 1e6 # g/L
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solvent_ind] / solvent_mw * 1e6 # g/L
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self._aq_solvent_rho = solvent_rho
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self._aq_solvent_rho = solvent_rho
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if extractant_rho is None:
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if extractant_rho is None:
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extractant_rho = mix_org(org_ind).partial_molar_volumes[
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extractant_rho = mix_org(org_ind).partial_molar_volumes[
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extractant_ind]/extractant_mw * 1e6
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extractant_ind] / extractant_mw * 1e6
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self._extractant_rho = extractant_rho
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self._extractant_rho = extractant_rho
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if diluant_rho is None:
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if diluant_rho is None:
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diluant_rho = mix_org(org_ind).partial_molar_volumes[
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diluant_rho = mix_org(org_ind).partial_molar_volumes[
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extractant_ind] / extractant_mw * 1e6
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extractant_ind] / extractant_mw * 1e6
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self._diluant_rho = diluant_rho
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self._diluant_rho = diluant_rho
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in_moles_data = []
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in_moles_data = []
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feed_vol = 1. # g/L
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aq_phase_solvent_moles = feed_vol * solvent_rho / solvent_mw
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aq_phase_solvent_moles = feed_vol * solvent_rho / solvent_mw
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for row in exp_df.values:
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for row in exp_df.values:
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h_plus_moles = feed_vol * row[0]
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h_plus_moles = feed_vol * row[0]
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@ -176,7 +217,7 @@ class REEPS:
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rare_earth_moles = feed_vol * row[6]
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rare_earth_moles = feed_vol * row[6]
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chlorine_moles = 3 * rare_earth_moles + h_plus_moles
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chlorine_moles = 3 * rare_earth_moles + h_plus_moles
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extractant_moles = feed_vol * row[3]
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extractant_moles = feed_vol * row[3]
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extractant_vol = extractant_moles * extractant_rho / extractant_mw
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extractant_vol = extractant_moles * extractant_mw / extractant_rho
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diluant_vol = feed_vol - extractant_vol
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diluant_vol = feed_vol - extractant_vol
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diluant_moles = diluant_vol * diluant_rho / diluant_mw
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diluant_moles = diluant_vol * diluant_rho / diluant_mw
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complex_moles = 0
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complex_moles = 0
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@ -196,3 +237,99 @@ class REEPS:
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def get_in_moles(self) -> pd.DataFrame:
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def get_in_moles(self) -> pd.DataFrame:
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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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h = x[0] * self._h_guess
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phases_copy = self._phases.copy()
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aq_ind = self._aq_ind
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org_ind = self._org_ind
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complex_name = self._complex_name
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rare_earth_ion_name = self._rare_earth_ion_name
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in_moles = self._in_moles
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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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complex_species = phases_copy[org_ind].species(complex_index)
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new_thermo_coeffs = complex_species.thermo.coeffs
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new_thermo_coeffs[1] = h
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complex_species.thermo = ct.ConstantCp(
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complex_species.thermo.min_temp,
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complex_species.thermo.max_temp,
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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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mix = ct.Mixture(phases_copy)
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pred = []
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for row in in_moles.values:
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mix.species_moles = row
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mix.equilibrate('TP', log_level=0)
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re_org = mix.species_moles[mix.species_index(
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org_ind, complex_name)]
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re_aq = mix.species_moles[mix.species_index(
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aq_ind, rare_earth_ion_name)]
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pred.append(np.log10(re_org / re_aq))
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pred = np.array(pred)
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meas = np.log10(exp_df['D(m)'].values)
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obj = np.sum((pred - meas) ** 2)
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return obj
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def fit(self, kwargs) -> float:
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"""Fits experimental to modeled data by estimating complex reference enthalpy
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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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"""
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x_guess = self._x_guess
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h_guess = self._h_guess
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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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return pred_complex_enthalpy
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def update_xml(self,
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complex_enthalpy,
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phases_xml_filename=None,
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complex_name=None):
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"""updates xml file with new complex_enthalpy"""
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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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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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root = tree.getroot()
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# Update xml file
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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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for h0 in species.iter('h0'):
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h0.text = str(complex_enthalpy)
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h0.set('updated', 'Updated at ' + time.strftime('%X'))
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tree.write(phases_xml_filename)
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def parity_plot(self):
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"""Parity plot between measured and predicted rare earth composition"""
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phases_copy = self._phases.copy()
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mix = ct.Mixture(phases_copy)
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aq_ind = self._aq_ind
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exp_df = self._exp_df
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in_moles = self._in_moles
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rare_earth_ion_name = self._rare_earth_ion_name
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pred = []
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for row in in_moles.values:
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mix.species_moles = row
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mix.equilibrate('TP', log_level=0)
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re_aq = mix.species_moles[mix.species_index(
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aq_ind, rare_earth_ion_name)]
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pred.append(re_aq)
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pred = np.array(pred)
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meas = exp_df['REeq(m)'].values
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min_data = np.min([pred, meas])
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max_data = np.max([pred, meas])
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min_max_data = np.array([min_data, max_data])
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fig, ax = plt.subplots()
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sns.scatterplot(meas, pred, color="r")
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sns.lineplot(min_max_data, min_max_data, color="b")
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ax.set(xlabel='Measured X equilibrium', ylabel='Predicted X equilibrium')
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plt.show()
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return None
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titusquah
5 years ago