Added docs and generalized to multiple species

tests/multi_ree_settings.txt

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+{"exp_csv_filename": "../data/csvs/Nd_exp_data.csv", "phases_xml_filename": "../data/xmls/twophase.xml", "opt_dict": {"Nd(H(A)2)3(org)": {"h0": -4662344.6400}}, "phase_names": ["HCl_electrolyte", "PC88A_liquid"], "aq_solvent_name": "H2O(L)", "extractant_name": "(HA)2(org)", "diluant_name": "dodecane", "complex_names": ["Nd(H(A)2)3(org)"], "rare_earth_ion_names": ["Nd+++"], "aq_solvent_rho": 1000.0, "extractant_rho": 960.0, "diluant_rho": 750.0}

tests/test_multi_reeps.py

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+import json
+import numpy as np
+import pyswarms as ps
+import sys
+sys.path.append('../')
+from reeps import REEPS1
+
+with open('multi_ree_settings.txt') as file:
+    testing_params = json.load(file)
+
+beaker = REEPS1(**testing_params)
+
+
+# def new_obj(predicted_dict, meas_df, epsilon):
+#     meas_cols = list(meas_df)
+#     pred_keys = list(predicted_dict.keys())
+#     meas = meas_df[meas_cols[2]]
+#     pred = (predicted_dict['re_org'] + epsilon) / (predicted_dict['re_aq'] + epsilon)
+#     log_pred = np.log10(pred)
+#     log_meas = np.log10(meas)
+#     obj = np.sum((log_pred - log_meas) ** 2)
+#     return obj
+# #
+# #
+# # def new_obj(ping):
+# #     print(ping)
+# beaker.set_objective_function(new_obj)
+# objective_kwargs = {"epsilon": 1e-14}
+# beaker.set
+# noinspection PyUnusedLocal
+def optimizer(func, x_guess):
+    lb = np.array([1e-1])
+    ub = np.array([1e1])
+    bounds = (lb, ub)
+    options = {'c1': 1e-3, 'c2': 1e-3, 'w': 0.9}
+    mini_optimizer = ps.single.global_best.GlobalBestPSO(n_particles=100, dimensions=1,
+                                                         options=options, bounds=bounds)
+    f_opt, x_opt = mini_optimizer.optimize(func, iters=100)
+
+    return x_opt
+
+
+minimizer_kwargs = {"method": 'SLSQP',
+                    "bounds": [(1e-1, 1e1)],
+                    "constraints": (),
+                    "options": {'disp': True, 'maxiter': 1000, 'ftol': 1e-6}}
+# est_enthalpy = beaker.fit(optimizer=optimizer)
+est_enthalpy = beaker.fit()
+print(est_enthalpy)
+
+# beaker.update_xml(est_enthalpy)
+# beaker.parity_plot()
+# print(beaker.r_squared())