diff --git a/.idea/workspace.xml b/.idea/workspace.xml index 4bb3c1f..3b6f98f 100644 --- a/.idea/workspace.xml +++ b/.idea/workspace.xml @@ -1,9 +1,30 @@ - - - + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - + - + @@ -416,7 +440,21 @@ @@ -454,7 +492,8 @@ - @@ -478,10 +517,10 @@ - + - + @@ -496,29 +535,37 @@ - - + + + + - - + + + + - - + + + + - - + + + + @@ -557,9 +604,10 @@ - - + + + @@ -577,9 +625,10 @@ - - + + + diff --git a/README.md b/README.md index c83f743..742d916 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ # REEPS -REEPS (Rare Earth Element Parameter Searcher) is a toolkit for estimating standard thermodynamic parameters for Gibbs minimization. -Extend a methodology for estimating standard thermodynamic parameters for Gibbs minimization in multiphase, multicomponent separations systems +LLEPE (Liquid-Liquid Extraction Parameter Estimator) is a toolkit for estimating standard thermodynamic parameters for Gibbs minimization. + ## Installation -To install REEPS, clone the repository with the command +To install llepe, clone the repository with the command ``` $ git clone https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git @@ -19,16 +19,42 @@ and run the command below in your terminal ``` $ pip install -e. ``` +For docs and tests, run +``` +$ pip install -e .[docs,tests] +``` ### Dependencies -REEPS uses packages: cantera (https://cantera.org/), pandas, numpy, scipy, xml, seaborn, and matplotlib +llepe uses packages: cantera (https://cantera.org/), pandas, numpy, scipy, xml, seaborn, and matplotlib ## Usage Check out examples in docs/examples + +Readthedocs documentation are in docs/build/html/index.html ```python -from reeps import REEPS -searcher = REEPS(**REEPS_parameters_dictionary) -optimized_parameter_dictionary = searcher.fit() -searcher.update_xml(optimized_parameter_dictionary) -searcher.parity_plot() -print(seacher.r_squared()) +from llepe import LLEPE + opt_dict = {'Nd(H(A)2)3(org)_h0': {'upper_element_name': 'species', + 'upper_attrib_name': 'name', + 'upper_attrib_value': 'Nd(H(A)2)3(org)', + 'lower_element_name': 'h0', + 'lower_attrib_name': None, + 'lower_attrib_value': None, + 'input_format': '{0}', + 'input_value': -4.7e6}} + + searcher_parameters = {'exp_data': 'Nd_exp_data.csv', + 'phases_xml_filename': 'twophase.xml', + 'opt_dict': opt_dict, + '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)'], + 'extracted_species_ion_names': ['Nd+++'], + 'aq_solvent_rho': 1000.0, + 'extractant_rho': 960.0, + 'diluant_rho': 750.0} + searcher = LLEPE(**searcher_parameters) + est_enthalpy = searcher.fit() + searcher.update_xml(est_enthalpy) + searcher.parity_plot(print_r_squared=True) ``` diff --git a/data/csvs/PC88A_HCL_NdPrCeLaDySmY.csv b/data/csvs/PC88A_HCL_NdPrCeLaDySmY.csv index b2646d3..bd7991a 100644 --- a/data/csvs/PC88A_HCL_NdPrCeLaDySmY.csv +++ b/data/csvs/PC88A_HCL_NdPrCeLaDySmY.csv @@ -10,16 +10,16 @@ Lyon (2016),0.01,0.01,1,1,0.259983361,0.197587354,0.315789474,0.088710553,0.0718 Lyon (2016),0.05,0.05,1,1,0.259983361,0.207986689,0.25,0.088710553,0.07540397,0.176470588,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 Lyon (2016),0.1,0.1,1,1,0.259983361,0.21578619,0.204819277,0.088710553,0.077178181,0.149425287,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 Lyon (2016),0.3,0.3,1,1,0.259983361,0.244384359,0.063829787,0.088710553,0.08338792,0.063829787,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -Liu (2014),1.00E-05,1.00E-05,0.1,0.1,0.022739878,0.017097653,0.33,0.008303308,0.006642646,0.25,0,0,0,0.054425491,0.050393973,0.08,0,0,0,0,0,0,0,0,0 -Liu (2014),1.00E-05,1.00E-05,0.3,0.3,0.022739878,0.013298174,0.71,0.008303308,0.005462702,0.52,0,0,0,0.054425491,0.048594188,0.12,0,0,0,0,0,0,0,0,0 -Liu (2014),1.00E-05,1.00E-05,0.5,0.5,0.022739878,0.010932634,1.08,0.008303308,0.004537327,0.83,0,0,0,0.054425491,0.048164151,0.13,0,0,0,0,0,0,0,0,0 -Liu (2014),1.00E-05,1.00E-05,0.7,0.7,0.022739878,0.009396644,1.42,0.008303308,0.003972875,1.09,0,0,0,0.054425491,0.047326514,0.15,0,0,0,0,0,0,0,0,0 -Liu (2014),1.00E-05,1.00E-05,0.9,0.9,0.022739878,0.008209342,1.77,0.008303308,0.002997584,1.77,0,0,0,0.054425491,0.045735706,0.19,0,0,0,0,0,0,0,0,0 -Banda (2014),1.00E-05,1.00E-05,0.1,0.1,0.022739878,0.018928042,0.201385664,0.008303308,0.007354823,0.128960943,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -Banda (2014),1.00E-05,1.00E-05,0.3,0.3,0.022739878,0.014333115,0.586527247,0.008303308,0.005999476,0.384005473,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -Banda (2014),1.00E-05,1.00E-05,0.5,0.5,0.022739878,0.010952454,1.076235839,0.008303308,0.004805359,0.727926764,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -Banda (2014),1.00E-05,1.00E-05,0.7,0.7,0.022739878,0.008786058,1.588177405,0.008303308,0.003974007,1.089404412,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -Banda (2014),1.00E-05,1.00E-05,0.9,0.9,0.022739878,0.00700602,2.245762712,0.008303308,0.00322327,1.576050934,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +Banda (2014),1.00E-05,1.00E-05,0.1,0.1,0.022739878,0.017097653,0.33,0.008303308,0.006642646,0.25,0,0,0,0.054425491,0.050393973,0.08,0,0,0,0,0,0,0,0,0 +Banda (2014),1.00E-05,1.00E-05,0.3,0.3,0.022739878,0.013298174,0.71,0.008303308,0.005462702,0.52,0,0,0,0.054425491,0.048594188,0.12,0,0,0,0,0,0,0,0,0 +Banda (2014),1.00E-05,1.00E-05,0.5,0.5,0.022739878,0.010932634,1.08,0.008303308,0.004537327,0.83,0,0,0,0.054425491,0.048164151,0.13,0,0,0,0,0,0,0,0,0 +Banda (2014),1.00E-05,1.00E-05,0.7,0.7,0.022739878,0.009396644,1.42,0.008303308,0.003972875,1.09,0,0,0,0.054425491,0.047326514,0.15,0,0,0,0,0,0,0,0,0 +Banda (2014),1.00E-05,1.00E-05,0.9,0.9,0.022739878,0.008209342,1.77,0.008303308,0.002997584,1.77,0,0,0,0.054425491,0.045735706,0.19,0,0,0,0,0,0,0,0,0 +Liu (2014),1.00E-05,1.00E-05,0.1,0.1,0.022739878,0.018928042,0.201385664,0.008303308,0.007354823,0.128960943,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +Liu (2014),1.00E-05,1.00E-05,0.3,0.3,0.022739878,0.014333115,0.586527247,0.008303308,0.005999476,0.384005473,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +Liu (2014),1.00E-05,1.00E-05,0.5,0.5,0.022739878,0.010952454,1.076235839,0.008303308,0.004805359,0.727926764,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +Liu (2014),1.00E-05,1.00E-05,0.7,0.7,0.022739878,0.008786058,1.588177405,0.008303308,0.003974007,1.089404412,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +Liu (2014),1.00E-05,1.00E-05,0.9,0.9,0.022739878,0.00700602,2.245762712,0.008303308,0.00322327,1.576050934,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 Kim (2012),0.01023293,0.01023293,0.1,0.1,0.009359401,0.007999488,0.17,0.003371001,0.003064546,0.1,0.038539496,0.037783819,0.02,0.022461314,0.022020896,0.02,0,0,0,0,0,0,0,0,0 Kim (2012),0.01023293,0.01023293,0.3,0.3,0.009359401,0.006881912,0.36,0.003371001,0.002763116,0.22,0.038539496,0.035357336,0.09,0.022461314,0.021597417,0.04,0,0,0,0,0,0,0,0,0 Kim (2012),0.01023293,0.01023293,0.5,0.5,0.009359401,0.005813293,0.61,0.003371001,0.002340973,0.44,0.038539496,0.032386131,0.19,0.022461314,0.02060671,0.09,0,0,0,0,0,0,0,0,0 diff --git a/data/xmls/PC88A_HCL_NdPrCeLaDySmY_w_pitzer.xml b/data/xmls/PC88A_HCL_NdPrCeLaDySmY_w_pitzer.xml index d2ad522..b218c2a 100644 --- a/data/xmls/PC88A_HCL_NdPrCeLaDySmY_w_pitzer.xml +++ b/data/xmls/PC88A_HCL_NdPrCeLaDySmY_w_pitzer.xml @@ -33,7 +33,7 @@ 298.14999999999998 - -1376882.3191117246 + -1376882.0784583509 558.9824 0.0 @@ -50,7 +50,7 @@ 298.14999999999998 - -4925566.309854757 + -4924298.0880370205 1117.965 0.0 @@ -67,7 +67,7 @@ 298.14999999999998 - -4938249.845712334 + -4935685.119723228 1117.965 0.0 @@ -85,7 +85,7 @@ 298.14999999999998 - -4920387.823199008 + -4920369.042961768 1117.965 0.0 @@ -103,7 +103,7 @@ 298.14999999999998 - -4933548.865580005 + -4928639.61964031 1117.965 0.0 @@ -120,7 +120,7 @@ 298.14999999999998 - -4932560.171447597 + -4931991.722599618 1117.965 0.0 @@ -138,7 +138,7 @@ 298.14999999999998 - -4944840.781582316 + -4944682.264585918 1117.965 0.0 @@ -157,7 +157,7 @@ 298.14999999999998 - -4924696.189921901 + -4924669.3217661735 1117.965 0.0 @@ -245,10 +245,10 @@ - 0.05879108748614492, 0.0, 0.0, 0.0, 0.0 - 0.5448324180244323, 0.0, 0.0, 0.0, 0.0 + 0.058791091500561485, 0.0, 0.0, 0.0, 0.0 + 0.5448322248125199, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.02066999867229882, 0.0, 0.0, 0.0, 0.0 + -0.02066999867229882, 0.0, 0.0, 0.0, 0.0 2 0 @@ -261,10 +261,10 @@ - 1.2137222016802447, 0.0, 0.0, 0.0, 0.0 - 7.748226963005033, 0.0, 0.0, 0.0, 0.0 + 1.213717095858249, 0.0, 0.0, 0.0, 0.0 + 7.7481294675488375, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.01963615126026457, 0.0, 0.0, 0.0, 0.0 + -0.01963615126026457, 0.0, 0.0, 0.0, 0.0 2 0 @@ -277,10 +277,10 @@ - 1.022316535866388, 0.0, 0.0, 0.0, 0.0 - 0.5296311209773129, 0.0, 0.0, 0.0, 0.0 + 1.0223168335791355, 0.0, 0.0, 0.0, 0.0 + 0.5296306654103653, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.024339999997603376, 0.0, 0.0, 0.0, 0.0 + -0.024339999997603376, 0.0, 0.0, 0.0, 0.0 2 0 @@ -293,10 +293,10 @@ - 0.7646397332938777, 0.0, 0.0, 0.0, 0.0 - 7.849320590516409, 0.0, 0.0, 0.0, 0.0 + 0.7646372240575223, 0.0, 0.0, 0.0, 0.0 + 7.849276225207628, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.019699989216349984, 0.0, 0.0, 0.0, 0.0 + -0.019699989216349984, 0.0, 0.0, 0.0, 0.0 2 0 @@ -309,10 +309,10 @@ - 0.2035235053232368, 0.0, 0.0, 0.0, 0.0 - 21.120426174002823, 0.0, 0.0, 0.0, 0.0 + 0.20352350320923904, 0.0, 0.0, 0.0, 0.0 + 21.120419048363047, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.02618999999473301, 0.0, 0.0, 0.0, 0.0 + -0.02618999999473301, 0.0, 0.0, 0.0, 0.0 2 0 @@ -325,10 +325,10 @@ - 0.8852802073165494, 0.0, 0.0, 0.0, 0.0 - 9.334653075341238, 0.0, 0.0, 0.0, 0.0 + 0.8852797060008407, 0.0, 0.0, 0.0, 0.0 + 9.334636294454038, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.015467323909969704, 0.0, 0.0, 0.0, 0.0 + -0.015467323909969704, 0.0, 0.0, 0.0, 0.0 2 0 @@ -341,10 +341,10 @@ - 0.6989081585234721, 0.0, 0.0, 0.0, 0.0 - 6.877882600430561, 0.0, 0.0, 0.0, 0.0 + 0.6989083059080712, 0.0, 0.0, 0.0, 0.0 + 6.877881736471866, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.019920000110321332, 0.0, 0.0, 0.0, 0.0 + -0.019920000110321332, 0.0, 0.0, 0.0, 0.0 2 0 diff --git a/data/xmls/twophase.xml b/data/xmls/twophase.xml index 1d0d109..3520b33 100644 --- a/data/xmls/twophase.xml +++ b/data/xmls/twophase.xml @@ -50,7 +50,7 @@ 298.14999999999998 - -4704699.156668724 + -4704699.156668724 1117.965 0.0 diff --git a/docs/Examples/iterative_fitter_eval_grapher.py b/docs/Examples/iterative_fitter_eval_grapher.py index aaed7bd..8d997c4 100644 --- a/docs/Examples/iterative_fitter_eval_grapher.py +++ b/docs/Examples/iterative_fitter_eval_grapher.py @@ -10,6 +10,9 @@ font = {'family': 'sans serif', matplotlib.rc('font', **font) plt.rc('xtick', labelsize=18) plt.rc('ytick', labelsize=18) +plt.rcParams['lines.linewidth'] = 4 +matplotlib.rcParams['lines.markersize'] = 10 + def ext_to_complex(h0, custom_obj_dict, mini_species): linear_params = custom_obj_dict['lin_param_df'] @@ -24,7 +27,8 @@ def mod_lin_param_df(lp_df, input_val, mini_species, mini_lin_param): return new_lp_df -info_df = pd.read_csv('outputs/iterative_fitter_output2.csv') +info_df = pd.read_csv('outputs/iterative_fitter_w_mse_output.csv') +test_row = 3 pitzer_params_filename = "../../data/jsons/min_h0_pitzer_params.txt" with open(pitzer_params_filename) as file: pitzer_params_dict = json.load(file) @@ -33,6 +37,8 @@ species_list = 'Nd,Pr,Ce,La,Dy,Sm,Y'.split(',') pitzer_param_list = ['beta0', 'beta1'] labeled_data = pd.read_csv("../../data/csvs/" "PC88A_HCL_NdPrCeLaDySmY.csv") +labeled_data = labeled_data.sort_values(['Feed Pr[M]', 'Feed Ce[M]'], + ascending=True) exp_data = labeled_data.drop(labeled_data.columns[0], axis=1) xml_file = "PC88A_HCL_NdPrCeLaDySmY_w_pitzer.xml" lin_param_df = pd.read_csv("../../data/csvs" @@ -76,11 +82,11 @@ info_dict = {'(HA)2(org)_h0': {'upper_element_name': 'species', 'lower_attrib_value': None, 'input_format': '{0}', 'input_value': - info_df.iloc[-1, :]['best_ext_h0']}} + info_df.iloc[test_row, :]['best_ext_h0']}} for species in species_list: for pitzer_param in pitzer_param_list: pitzer_str = "{0}_{1}".format(species, pitzer_param) - value = info_df.iloc[-1, :][pitzer_str] + value = info_df.iloc[test_row, :][pitzer_str] pitzer_params_dict[pitzer_str]['input_value'] = value lin_str = "{0}_slope".format(species) inner_dict = {'custom_object_name': 'lin_param_df', @@ -91,7 +97,7 @@ for species in species_list: } info_dict[lin_str] = inner_dict lin_str = "{0}_intercept".format(species) - value = info_df.iloc[-1, :][lin_str] + value = info_df.iloc[test_row, :][lin_str] inner_dict = {'custom_object_name': 'lin_param_df', 'function': mod_lin_param_df, 'kwargs': {'mini_species': species, @@ -112,15 +118,52 @@ for col in exp_data.columns: if 'aq_i' in col: feed_cols.append(col) exp_data['total_re'] = exp_data[feed_cols].sum(axis=1) +label_list = [] +for index, row in exp_data[feed_cols].iterrows(): + bool_list = list((row > 0).values) + label = '' + for species, el in zip(species_list, bool_list): + if el: + label = '{0}-{1}'.format(label, species) + label = label[1:] + label_list.append(label) +r2s = "" for species in species_list: - save_name = 'outputs/parity_iterative_fitter_{0}_org_eq'.format(species) + # if species=='La': + # save_name = 'outputs' \ + # '/parity_iterative_fitter_{0}_org_eq'.format(species) + save_name = None + # fig, ax = estimator.parity_plot('{0}_org_eq'.format(species), + # c_data='z_i', + # c_label='Feed total RE ' + # 'molarity (mol/L)', + # print_r_squared=True, + # save_path=save_name) + r2s += str(estimator.r_squared('{0}_org_eq'.format(species))) + ',' + fig, ax = estimator.parity_plot('{0}_org_eq'.format(species), - c_data=exp_data[ - 'total_re'].values, - c_label='Feed total RE ' - 'molarity (mol/L)', + data_labels=label_list, print_r_squared=True, save_path=save_name) + ax.legend(loc=4) +pred_df = pd.DataFrame(estimator.get_predicted_dict()) +new_cols = [] +for col in pred_df.columns: + new_cols.append("pred_{0}".format(col)) +pred_df.columns = new_cols +new_cols = ['label', + 'h_i', + 'h_eq', + 'z_i', + 'z_eq' + ] +for species in species_list: + new_cols.append("{0}_aq_i".format(species)) + new_cols.append("{0}_aq_eq".format(species)) + new_cols.append("{0}_d_eq".format(species)) +labeled_data.columns = new_cols +total_df = labeled_data.join(pred_df) +# total_df.to_csv('if_mse_total_df.csv') # short_info_dict = {} # for key, value in info_dict.items(): # short_info_dict[key] = value['input_value'] diff --git a/docs/Examples/outputs/temp.xml b/docs/Examples/outputs/temp.xml index e292885..b218c2a 100644 --- a/docs/Examples/outputs/temp.xml +++ b/docs/Examples/outputs/temp.xml @@ -33,7 +33,7 @@ 298.14999999999998 - -1376882.3191117246 + -1376882.0784583509 558.9824 0.0 @@ -50,7 +50,7 @@ 298.14999999999998 - -4925566.309854757 + -4924298.0880370205 1117.965 0.0 @@ -67,7 +67,7 @@ 298.14999999999998 - -4938249.845712334 + -4935685.119723228 1117.965 0.0 @@ -85,7 +85,7 @@ 298.14999999999998 - -4920387.823199008 + -4920369.042961768 1117.965 0.0 @@ -103,7 +103,7 @@ 298.14999999999998 - -4933548.865580005 + -4928639.61964031 1117.965 0.0 @@ -120,7 +120,7 @@ 298.14999999999998 - -4932560.171447597 + -4931991.722599618 1117.965 0.0 @@ -138,7 +138,7 @@ 298.14999999999998 - -4944840.781582316 + -4944682.264585918 1117.965 0.0 @@ -157,7 +157,7 @@ 298.14999999999998 - -4924696.189921901 + -4924669.3217661735 1117.965 0.0 @@ -245,10 +245,10 @@ - 0.05879108748614492, 0.0, 0.0, 0.0, 0.0 - 0.5448324180244323, 0.0, 0.0, 0.0, 0.0 + 0.058791091500561485, 0.0, 0.0, 0.0, 0.0 + 0.5448322248125199, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.02066999867229882, 0.0, 0.0, 0.0, 0.0 + -0.02066999867229882, 0.0, 0.0, 0.0, 0.0 2 0 @@ -261,10 +261,10 @@ - 1.2137222016802447, 0.0, 0.0, 0.0, 0.0 - 7.748226963005033, 0.0, 0.0, 0.0, 0.0 + 1.213717095858249, 0.0, 0.0, 0.0, 0.0 + 7.7481294675488375, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.01963615126026457, 0.0, 0.0, 0.0, 0.0 + -0.01963615126026457, 0.0, 0.0, 0.0, 0.0 2 0 @@ -277,10 +277,10 @@ - 1.022316535866388, 0.0, 0.0, 0.0, 0.0 - 0.5296311209773129, 0.0, 0.0, 0.0, 0.0 + 1.0223168335791355, 0.0, 0.0, 0.0, 0.0 + 0.5296306654103653, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.024339999997603376, 0.0, 0.0, 0.0, 0.0 + -0.024339999997603376, 0.0, 0.0, 0.0, 0.0 2 0 @@ -293,10 +293,10 @@ - 0.7646397332938777, 0.0, 0.0, 0.0, 0.0 - 7.849320590516409, 0.0, 0.0, 0.0, 0.0 + 0.7646372240575223, 0.0, 0.0, 0.0, 0.0 + 7.849276225207628, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.019699989216349984, 0.0, 0.0, 0.0, 0.0 + -0.019699989216349984, 0.0, 0.0, 0.0, 0.0 2 0 @@ -309,10 +309,10 @@ - 0.2035235053232368, 0.0, 0.0, 0.0, 0.0 - 21.120426174002823, 0.0, 0.0, 0.0, 0.0 + 0.20352350320923904, 0.0, 0.0, 0.0, 0.0 + 21.120419048363047, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.02618999999473301, 0.0, 0.0, 0.0, 0.0 + -0.02618999999473301, 0.0, 0.0, 0.0, 0.0 2 0 @@ -325,10 +325,10 @@ - 0.8852802073165494, 0.0, 0.0, 0.0, 0.0 - 9.334653075341238, 0.0, 0.0, 0.0, 0.0 + 0.8852797060008407, 0.0, 0.0, 0.0, 0.0 + 9.334636294454038, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.015467323909969704, 0.0, 0.0, 0.0, 0.0 + -0.015467323909969704, 0.0, 0.0, 0.0, 0.0 2 0 @@ -341,10 +341,10 @@ - 0.6989081585234721, 0.0, 0.0, 0.0, 0.0 - 6.877882600430561, 0.0, 0.0, 0.0, 0.0 + 0.6989083059080712, 0.0, 0.0, 0.0, 0.0 + 6.877881736471866, 0.0, 0.0, 0.0, 0.0 0.0, 0.0, 0.0, 0.0, 0.0 - -0.019920000110321332, 0.0, 0.0, 0.0, 0.0 + -0.019920000110321332, 0.0, 0.0, 0.0, 0.0 2 0 diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle index 176b86d..bfa0d33 100644 Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ diff --git a/docs/build/doctrees/guide/install.doctree b/docs/build/doctrees/guide/install.doctree index 3291873..46eb899 100644 Binary files a/docs/build/doctrees/guide/install.doctree and b/docs/build/doctrees/guide/install.doctree differ diff --git a/docs/build/doctrees/guide/quickstart.doctree b/docs/build/doctrees/guide/quickstart.doctree index 149c9f1..3f643f7 100644 Binary files a/docs/build/doctrees/guide/quickstart.doctree and b/docs/build/doctrees/guide/quickstart.doctree differ diff --git a/docs/build/doctrees/modules/reeps.doctree b/docs/build/doctrees/modules/reeps.doctree index 55a0dd7..e316e1a 100644 Binary files a/docs/build/doctrees/modules/reeps.doctree and b/docs/build/doctrees/modules/reeps.doctree differ diff --git a/docs/build/html/_images/quick_start_output.png b/docs/build/html/_images/quick_start_output.png new file mode 100644 index 0000000..eefb412 Binary files /dev/null and b/docs/build/html/_images/quick_start_output.png differ diff --git a/docs/build/html/_modules/llepe/llepe.html b/docs/build/html/_modules/llepe/llepe.html index 06aabe6..bf78f9b 100644 --- a/docs/build/html/_modules/llepe/llepe.html +++ b/docs/build/html/_modules/llepe/llepe.html @@ -159,7 +159,6 @@ from scipy.optimize import minimize # noinspection PyPep8Naming import xml.etree.ElementTree as ET -import seaborn as sns import matplotlib.pyplot as plt import shutil import copy @@ -169,9 +168,6 @@ import pkg_resources from .utils import set_size -sns.set() -sns.set(font_scale=1.6) -
[docs]class LLEPE: r""" @@ -285,7 +281,8 @@ :param extracted_species_list: (list) names of extracted species elements. If ``None``, extracted_species_list will be extracted_species_ion_names - without '+' i.e. 'Nd+++'->'Nd' + without '+' i.e. 'Nd+++'->'Nd' + :param aq_solvent_rho: (float) density of solvent (g/L) If ``None``, molar volume/molecular weight is used from xml @@ -413,12 +410,22 @@ 'function', 'kwargs', and 'independent_params. 'function' is a function of the form - ``function(independent_param__value_list, **kwargs)`` + + ``function(independent_param__value_list, custom_objects_dict, + **kwargs)`` + 'kwargs' are the extra arguments to pass to function + 'independent_params' is a list of parameter names in opt_dict that the dependent_param is a function of. + 'custom_objects_dict' is for accessing the estimator's internal + custom_objects_dict and must be included in the arguments, even if the + custom_objects_dict is not set and is None. + See example code for usage. + :param custom_objects_dict: (dict) dictionary containing custom objects + format: {<object_name_string>: <object>,...} """ def __init__(self, @@ -436,12 +443,13 @@ diluant_rho=None, opt_dict=None, objective_function='Log-MSE', - optimizer='SLSQP', + optimizer='scipy_minimize', temp_xml_file_path=None, dependant_params_dict=None, + custom_objects_dict=None ): self._built_in_obj_list = ['Log-MSE'] - self._built_in_opt_list = ['SLSQP'] + self._built_in_opt_list = ['scipy_minimize'] self._exp_data = exp_data self._phases_xml_filename = phases_xml_filename self._opt_dict = opt_dict @@ -463,6 +471,7 @@ temp_xml_file_path = r'{0}/temp.xml'.format(os.getenv('TEMP')) self._temp_xml_file_path = temp_xml_file_path self._dependant_params_dict = dependant_params_dict + self._custom_objects_dict = custom_objects_dict # Try and except for adding package data to path. # This only works for sdist, not bdist # If bdist is needed, research "manifest.in" python setup files @@ -474,7 +483,7 @@ except FileNotFoundError: self._phases_xml_filename = \ pkg_resources.resource_filename('llepe', - r'..\data\xmls\{0}'.format( + '../data/xmls/{0}'.format( phases_xml_filename)) shutil.copyfile(self._phases_xml_filename, self._temp_xml_file_path) @@ -485,7 +494,7 @@ self._exp_df = pd.read_csv(self._exp_data) except FileNotFoundError: self._exp_data = pkg_resources.resource_filename( - 'llepe', r'..\data\csvs\{0}'.format(self._exp_data)) + 'llepe', '../data/csvs/{0}'.format(self._exp_data)) self._exp_df = pd.read_csv(self._exp_data) else: self._exp_df = self._exp_data.copy() @@ -600,7 +609,7 @@ self._exp_df = pd.read_csv(self._exp_data) except FileNotFoundError: self._exp_data = pkg_resources.resource_filename( - 'llepe', r'..\data\csvs\{0}'.format(self._exp_data)) + 'llepe', '../data/csvs/{0}'.format(self._exp_data)) self._exp_df = pd.read_csv(self._exp_data) else: self._exp_df = exp_data.copy() @@ -654,7 +663,7 @@ except FileNotFoundError: self._phases_xml_filename = \ pkg_resources.resource_filename('llepe', - r'..\data\xmls\{0}'.format( + '../data/xmls/{0}'.format( phases_xml_filename)) shutil.copyfile(self._phases_xml_filename, self._temp_xml_file_path) @@ -998,7 +1007,7 @@ "optimizer must be a function " "with at least 2 arguments: " "f(objective_func,x_guess, kwargs)") - if optimizer == 'SLSQP': + if optimizer == 'scipy_minimize': optimizer = self.scipy_minimize self._optimizer = optimizer return None
@@ -1037,6 +1046,7 @@
[docs] def get_dependant_params_dict(self): """ Returns the dependant_params_dict + :return: dependant_params_dict: (dict) dictionary containing information about parameters dependant on opt_dict """ @@ -1045,12 +1055,32 @@
[docs] def set_dependant_params_dict(self, dependant_params_dict): """ Sets the dependant_params_dict + :param dependant_params_dict: (dict) dictionary containing information - about parameters dependant on opt_dict + about parameters dependant on opt_dict """ self._dependant_params_dict = dependant_params_dict return None
+
[docs] def get_custom_objects_dict(self): + """ + Returns the custom_objects_dict + + :return: custom_objects_dict: (dict) dictionary containing + information about custom objects from user + """ + return self._custom_objects_dict
+ +
[docs] def set_custom_objects_dict(self, custom_objects_dict): + """ + Sets the custom_objects_dict + + :param custom_objects_dict: (dict) dictionary containing information + about about custom objects from user + """ + self._custom_objects_dict = custom_objects_dict + return None
+
[docs] def update_predicted_dict(self, phases_xml_filename=None, phase_names=None): @@ -1143,6 +1173,7 @@ objective_function = self._objective_function opt_dict = copy.deepcopy(self._opt_dict) dep_dict = copy.deepcopy(self._dependant_params_dict) + custom_objects_dict = copy.deepcopy(self._custom_objects_dict) x = np.array(x) if len(x.shape) == 1: @@ -1158,6 +1189,8 @@ x[ind]): # if nan, do not update xml with nan opt_dict[param_name]['input_value'] *= x[ind] + if custom_objects_dict is not None: + self.update_custom_objects_dict(opt_dict) self.update_xml(opt_dict, temp_xml_file_path, dependant_params_dict=dep_dict) @@ -1228,8 +1261,8 @@ dependant_params_dict=None): """updates xml file with info_dict - :param info_dict: (dict) info in {species_names:{thermo_prop:val}} - Requires an identical structure to opt_dict + :param info_dict: (dict) Requires an identical structure to opt_dict + Ignores items with keys containing "custom_object_name" :param phases_xml_filename: (str) xml filename if editing other xml If ``None``, the current xml will be modified and the internal Cantera phases will be refreshed to the new values. @@ -1239,7 +1272,8 @@ if phases_xml_filename is None: phases_xml_filename = self._phases_xml_filename new_dict = copy.deepcopy(info_dict) - dep_dict = dependant_params_dict + dep_dict = copy.deepcopy(dependant_params_dict) + custom_objects_dict = copy.deepcopy(self._custom_objects_dict) if dep_dict is not None: new_dict.update(dep_dict) @@ -1257,10 +1291,12 @@ ind_vals = [new_dict[ind_param_name]['input_value'] for ind_param_name in ind_param_names] if mod_kwargs is None: - new_dict[param_name]['input_value'] = mod_func(ind_vals) - else: new_dict[param_name]['input_value'] = \ mod_func(ind_vals, + custom_objects_dict) + else: + new_dict[param_name]['input_value'] = \ + mod_func(ind_vals, custom_objects_dict, **mod_kwargs) tree = ET.parse(phases_xml_filename) root = tree.getroot() @@ -1268,6 +1304,8 @@ for key in list(new_dict.keys()): d = new_dict[key] now = datetime.now() + if 'custom_object_name' in list(d.keys()): + continue if (d['upper_attrib_name'] is not None and d['lower_attrib_name'] is not None): for child1 in root.iter(d['upper_element_name']): @@ -1324,6 +1362,31 @@ self.set_phases(self._phases_xml_filename, self._phase_names) return None
+
[docs] def update_custom_objects_dict(self, info_dict): + """ + updates internal custom_objects_dict with info_dict + + :param info_dict: Requires an identical structure to opt_dict + Ignores items with keys containing "custom_object_name" + + :return: None + """ + custom_objects_dict = copy.deepcopy(self._custom_objects_dict) + for key in list(info_dict.keys()): + d = info_dict[key] + if 'upper_element_name' in list(d.keys()): + continue + func = d['function'] + value = d['input_value'] + kwargs = d['kwargs'] + object_name = d['custom_object_name'] + new_object = func(custom_objects_dict[object_name], + value, + **kwargs) + custom_objects_dict[object_name] = new_object + self._custom_objects_dict = custom_objects_dict + return None
+
[docs] def parity_plot(self, compared_value=None, c_data=None, @@ -1388,6 +1451,11 @@ 'meas': meas, c_data: exp_df[c_data].values, 'feed_molarity': feed_molarity}) + elif c_data is not None: + combined_df = pd.DataFrame({'pred': pred, + 'meas': meas, + 'c_data': c_data, + 'feed_molarity': feed_molarity}) else: combined_df = pd.DataFrame({'pred': pred, 'meas': meas, @@ -1420,35 +1488,36 @@ default_title = '{0} complex eq. conc. (mol/L)'.format( compared_species) fig, ax = plt.subplots() + if isinstance(data_labels, list): unique_labels = list(set(data_labels)) for label in unique_labels: filtered_data = combined_df[combined_df['label'] == label] filtered_meas = filtered_data['meas'] filtered_pred = filtered_data['pred'] - ax.scatter(filtered_meas, filtered_pred, label=label) + if len(filtered_pred) != 0: + ax.scatter(filtered_meas, filtered_pred, label=label) if legend: ax.legend(loc='best') elif c_data is not None: if isinstance(c_data, str): c_data = combined_df[c_data].values + else: + c_data = combined_df['c_data'].values p1 = ax.scatter(meas, pred, c=c_data, alpha=1, cmap='viridis') c_bar = fig.colorbar(p1, format='%.2f') if c_label is not None: c_bar.set_label(c_label, rotation=270, labelpad=20) else: - sns.scatterplot(meas, pred, color="r", - legend=False) + ax.scatter(meas, pred, c="r", label="") + ax.plot(min_max_data, min_max_data, color="b", label="") if print_r_squared: ax.text(min_max_data[0], min_max_data[1] * 0.9, '$R^2$={0:.2f}'.format(self.r_squared(compared_value))) - # plt.legend(loc='lower right') - # else: - # plt.legend() ax.set(xlabel='Measured', ylabel='Predicted') if plot_title is None: diff --git a/docs/build/html/_sources/guide/install.rst.txt b/docs/build/html/_sources/guide/install.rst.txt index 8486537..ce1a1f9 100644 --- a/docs/build/html/_sources/guide/install.rst.txt +++ b/docs/build/html/_sources/guide/install.rst.txt @@ -8,7 +8,7 @@ Installation Prerequisites ============= -REEPS requires python3 (>=3.5) with the development headers. +LLEPE requires python3 (>=3.5) with the development headers. Stable Release diff --git a/docs/build/html/_sources/guide/quickstart.rst.txt b/docs/build/html/_sources/guide/quickstart.rst.txt index 2ccdbd8..8e2c250 100644 --- a/docs/build/html/_sources/guide/quickstart.rst.txt +++ b/docs/build/html/_sources/guide/quickstart.rst.txt @@ -9,28 +9,41 @@ Here is a quick example of how to fit an xml thermodynamic model to experimental This code fits Nd standard enthalpy in the "twophase.xml" cantera file to the experimental data in "Nd_exp_data.csv". +This code requires that you copy and paste the "elementz.xml" file in the llepe's data folder into +the Cantera's data folder located in your environments site-packages folder. + The code then produces a parity plot of the measured and predicted concentrations of Nd 3+ in the aqueous phase. .. code-block:: python - from reeps import REEPS + from llepe import LLEPE + opt_dict = {'Nd(H(A)2)3(org)_h0': {'upper_element_name': 'species', + 'upper_attrib_name': 'name', + 'upper_attrib_value': 'Nd(H(A)2)3(org)', + 'lower_element_name': 'h0', + 'lower_attrib_name': None, + 'lower_attrib_value': None, + 'input_format': '{0}', + 'input_value': -4.7e6}} - searcher_parameters = {'exp_csv_filename': 'Nd_exp_data.csv', + searcher_parameters = {'exp_data': 'Nd_exp_data.csv', 'phases_xml_filename': 'twophase.xml', - 'opt_dict': {'Nd(H(A)2)3(org)': {'h0': -4.7e6}}, + 'opt_dict': opt_dict, '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+++'], + 'extracted_species_ion_names': ['Nd+++'], 'aq_solvent_rho': 1000.0, 'extractant_rho': 960.0, 'diluant_rho': 750.0} - searcher = REEPS(**searcher_parameters) + searcher = LLEPE(**searcher_parameters) est_enthalpy = searcher.fit() searcher.update_xml(est_enthalpy) searcher.parity_plot(print_r_squared=True) The code should return something like this + +.. figure:: ../_static/img/quick_start_output.png \ No newline at end of file diff --git a/docs/build/html/_static/img/quick_start_output.png b/docs/build/html/_static/img/quick_start_output.png new file mode 100644 index 0000000..eefb412 Binary files /dev/null and b/docs/build/html/_static/img/quick_start_output.png differ diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html index d1e1f7b..03c3e8d 100644 --- a/docs/build/html/genindex.html +++ b/docs/build/html/genindex.html @@ -182,6 +182,8 @@
  • get_aq_solvent_rho() (llepe.LLEPE method)
  • get_complex_names() (llepe.LLEPE method) +
    • +
  • get_custom_objects_dict() (llepe.LLEPE method)
  • get_dependant_params_dict() (llepe.LLEPE method)
    • @@ -192,11 +194,11 @@
  • get_exp_df() (llepe.LLEPE method)
  • get_extractant_name() (llepe.LLEPE method) -
    • -
  • get_extractant_rho() (llepe.LLEPE method)
      • +
    • set_extractant_name() (llepe.LLEPE method) +
    • set_extractant_rho() (llepe.LLEPE method)
    • set_extracted_species_ion_names() (llepe.LLEPE method) @@ -317,10 +321,12 @@

      U

      diff --git a/docs/build/html/guide/install.html b/docs/build/html/guide/install.html index 0eed037..f28dddc 100644 --- a/docs/build/html/guide/install.html +++ b/docs/build/html/guide/install.html @@ -166,7 +166,7 @@

      Installation

      Prerequisites

      -

      REEPS requires python3 (>=3.5) with the development headers.

      +

      LLEPE requires python3 (>=3.5) with the development headers.

      Stable Release

      diff --git a/docs/build/html/guide/quickstart.html b/docs/build/html/guide/quickstart.html index ed14293..948381e 100644 --- a/docs/build/html/guide/quickstart.html +++ b/docs/build/html/guide/quickstart.html @@ -160,29 +160,42 @@

      Here is a quick example of how to fit an xml thermodynamic model to experimental data.

      This code fits Nd standard enthalpy in the "twophase.xml" cantera file to the experimental data in "Nd_exp_data.csv".

      +

      This code requires that you copy and paste the "elementz.xml" file in the llepe's data folder into +the Cantera's data folder located in your environments site-packages folder.

      The code then produces a parity plot of the measured and predicted concentrations of Nd 3+ in the aqueous phase.

      -
      from reeps import REEPS
-
-searcher_parameters = {'exp_csv_filename': 'Nd_exp_data.csv',
+
      from llepe import LLEPE
+opt_dict = {'Nd(H(A)2)3(org)_h0': {'upper_element_name': 'species',
+                      'upper_attrib_name': 'name',
+                      'upper_attrib_value': 'Nd(H(A)2)3(org)',
+                      'lower_element_name': 'h0',
+                      'lower_attrib_name': None,
+                      'lower_attrib_value': None,
+                      'input_format': '{0}',
+                      'input_value': -4.7e6}}
+
+searcher_parameters = {'exp_data': 'Nd_exp_data.csv',
                                            'phases_xml_filename': 'twophase.xml',
-                                           'opt_dict': {'Nd(H(A)2)3(org)': {'h0': -4.7e6}},
+                                           'opt_dict': opt_dict,
                                            '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+++'],
+                                           'extracted_species_ion_names': ['Nd+++'],
                                            'aq_solvent_rho': 1000.0,
                                            'extractant_rho': 960.0,
                                            'diluant_rho': 750.0}
-searcher = REEPS(**searcher_parameters)
+searcher = LLEPE(**searcher_parameters)
 est_enthalpy = searcher.fit()
 searcher.update_xml(est_enthalpy)
 searcher.parity_plot(print_r_squared=True)
 
      
 
      
 
      The code should return something like this
      
+
      
+../_images/quick_start_output.png
+
      diff --git a/docs/build/html/modules/reeps.html b/docs/build/html/modules/reeps.html index 7e84d0e..9275abb 100644 --- a/docs/build/html/modules/reeps.html +++ b/docs/build/html/modules/reeps.html @@ -163,7 +163,7 @@

      Parameters

      -class llepe.LLEPE(exp_data, phases_xml_filename, phase_names, aq_solvent_name, extractant_name, diluant_name, complex_names, extracted_species_ion_names, extracted_species_list=None, aq_solvent_rho=None, extractant_rho=None, diluant_rho=None, opt_dict=None, objective_function='Log-MSE', optimizer='SLSQP', temp_xml_file_path=None, dependant_params_dict=None)[source]
      +class llepe.LLEPE(exp_data, phases_xml_filename, phase_names, aq_solvent_name, extractant_name, diluant_name, complex_names, extracted_species_ion_names, extracted_species_list=None, aq_solvent_rho=None, extractant_rho=None, diluant_rho=None, opt_dict=None, objective_function='Log-MSE', optimizer='scipy_minimize', temp_xml_file_path=None, dependant_params_dict=None, custom_objects_dict=None)[source]

      Liquid-Liquid Extraction Parameter estimator

      Note

      @@ -277,10 +277,8 @@ i.e. Nd(H(A)2)3(org), Pr(H(A)2)3(org)

    • extracted_species_ion_names -- (list) names of extracted species ions in xml file

    • extracted_species_list --

      (list) names of extracted species elements.

      -
      -
      If None, extracted_species_list will be extracted_species_ion_names

      without '+' i.e. 'Nd+++'->'Nd'

      -
      -
      +

      If None, extracted_species_list will be extracted_species_ion_names +without '+' i.e. 'Nd+++'->'Nd'

    • aq_solvent_rho --

      (float) density of solvent (g/L)

      If None, molar volume/molecular weight is used from xml

      @@ -402,13 +400,19 @@ xml file

      about parameters dependant on opt_dict. Has a similar structure to opt_dict except instead of input values, it has 3 other fields: 'function', 'kwargs', and 'independent_params.

      -

      'function' is a function of the form -function(independent_param__value_list, **kwargs) -'kwargs' are the extra arguments to pass to function -'independent_params' is a list of parameter names in opt_dict that the +

      'function' is a function of the form

      +

      function(independent_param__value_list, custom_objects_dict, +**kwargs)

      +

      'kwargs' are the extra arguments to pass to function

      +

      'independent_params' is a list of parameter names in opt_dict that the dependent_param is a function of.

      +

      'custom_objects_dict' is for accessing the estimator's internal +custom_objects_dict and must be included in the arguments, even if the +custom_objects_dict is not set and is None.

      See example code for usage.

      • +

    • custom_objects_dict -- (dict) dictionary containing custom objects +format: {<object_name_string>: <object>,...}

      • @@ -469,14 +473,28 @@ optimized opt_dict: Has identical structure as opt_dict

      +
      +
      +get_custom_objects_dict()[source]
      +

      Returns the custom_objects_dict

      +
      +
      Returns
      +

      custom_objects_dict: (dict) dictionary containing +information about custom objects from user

      +
      +
      +
      +
      get_dependant_params_dict()[source]
      -

      Returns the dependant_params_dict -:return: dependant_params_dict: (dict) dictionary containing

      -
      -

      information about parameters dependant on opt_dict

      -
      +

      Returns the dependant_params_dict

      +
      +
      Returns
      +

      dependant_params_dict: (dict) dictionary containing +information about parameters dependant on opt_dict

      +
      +
      @@ -795,12 +813,28 @@ objective_function value

      +
      +
      +set_custom_objects_dict(custom_objects_dict)[source]
      +

      Sets the custom_objects_dict

      +
      +
      Parameters
      +

      custom_objects_dict -- (dict) dictionary containing information +about about custom objects from user

      +
      +
      +
      +
      set_dependant_params_dict(dependant_params_dict)[source]
      -

      Sets the dependant_params_dict -:param dependant_params_dict: (dict) dictionary containing information +

      Sets the dependant_params_dict

      +
      +
      Parameters
      +

      dependant_params_dict -- (dict) dictionary containing information about parameters dependant on opt_dict

      +
      +
      @@ -979,6 +1013,21 @@ xml file.

      +
      +
      +update_custom_objects_dict(info_dict)[source]
      +

      updates internal custom_objects_dict with info_dict

      +
      +
      Parameters
      +

      info_dict -- Requires an identical structure to opt_dict +Ignores items with keys containing "custom_object_name"

      +
      +
      Returns
      +

      None

      +
      +
      +
      +
      update_predicted_dict(phases_xml_filename=None, phase_names=None)[source]
      @@ -1005,8 +1054,8 @@ If None
      Parameters
        -

      • info_dict -- (dict) info in {species_names:{thermo_prop:val}} -Requires an identical structure to opt_dict

        • +

      • info_dict -- (dict) Requires an identical structure to opt_dict +Ignores items with keys containing "custom_object_name"

      • phases_xml_filename -- (str) xml filename if editing other xml If None, the current xml will be modified and the internal Cantera phases will be refreshed to the new values.

        • diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv index b30397f..4f45eec 100644 Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js index b0d14de..d5abc95 100644 --- a/docs/build/html/searchindex.js +++ b/docs/build/html/searchindex.js @@ -1 +1 @@ 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Started","Welcome to llepe's docs! - the Liquid-Liquid Extraction Parameter Estimator","LLEPE"],titleterms:{Using:0,bleed:0,develop:0,doc:2,docker:0,earth:[],edg:0,element:[],estim:2,extract:2,get:1,imag:0,indic:2,instal:0,liquid:2,llepe:[2,3],paramet:[2,3],prerequisit:0,rare:[],reep:[],releas:0,searcher:[],stabl:0,start:1,tabl:2,version:0,welcom:2}}) \ No newline at end of file diff --git a/docs/source/_static/img/quick_start_output.png b/docs/source/_static/img/quick_start_output.png new file mode 100644 index 0000000..eefb412 Binary files /dev/null and b/docs/source/_static/img/quick_start_output.png differ diff --git a/docs/source/guide/install.rst b/docs/source/guide/install.rst index 8486537..ce1a1f9 100644 --- a/docs/source/guide/install.rst +++ b/docs/source/guide/install.rst @@ -8,7 +8,7 @@ Installation Prerequisites ============= -REEPS requires python3 (>=3.5) with the development headers. +LLEPE requires python3 (>=3.5) with the development headers. Stable Release diff --git a/docs/source/guide/quickstart.rst b/docs/source/guide/quickstart.rst index 2ccdbd8..8e2c250 100644 --- a/docs/source/guide/quickstart.rst +++ b/docs/source/guide/quickstart.rst @@ -9,28 +9,41 @@ Here is a quick example of how to fit an xml thermodynamic model to experimental This code fits Nd standard enthalpy in the "twophase.xml" cantera file to the experimental data in "Nd_exp_data.csv". +This code requires that you copy and paste the "elementz.xml" file in the llepe's data folder into +the Cantera's data folder located in your environments site-packages folder. + The code then produces a parity plot of the measured and predicted concentrations of Nd 3+ in the aqueous phase. .. code-block:: python - from reeps import REEPS + from llepe import LLEPE + opt_dict = {'Nd(H(A)2)3(org)_h0': {'upper_element_name': 'species', + 'upper_attrib_name': 'name', + 'upper_attrib_value': 'Nd(H(A)2)3(org)', + 'lower_element_name': 'h0', + 'lower_attrib_name': None, + 'lower_attrib_value': None, + 'input_format': '{0}', + 'input_value': -4.7e6}} - searcher_parameters = {'exp_csv_filename': 'Nd_exp_data.csv', + searcher_parameters = {'exp_data': 'Nd_exp_data.csv', 'phases_xml_filename': 'twophase.xml', - 'opt_dict': {'Nd(H(A)2)3(org)': {'h0': -4.7e6}}, + 'opt_dict': opt_dict, '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+++'], + 'extracted_species_ion_names': ['Nd+++'], 'aq_solvent_rho': 1000.0, 'extractant_rho': 960.0, 'diluant_rho': 750.0} - searcher = REEPS(**searcher_parameters) + searcher = LLEPE(**searcher_parameters) est_enthalpy = searcher.fit() searcher.update_xml(est_enthalpy) searcher.parity_plot(print_r_squared=True) The code should return something like this + +.. figure:: ../_static/img/quick_start_output.png \ No newline at end of file diff --git a/llepe/llepe.py b/llepe/llepe.py index ba5e628..7a12f67 100644 --- a/llepe/llepe.py +++ b/llepe/llepe.py @@ -127,7 +127,8 @@ class LLEPE: :param extracted_species_list: (list) names of extracted species elements. If ``None``, extracted_species_list will be extracted_species_ion_names - without '+' i.e. 'Nd+++'->'Nd' + without '+' i.e. 'Nd+++'->'Nd' + :param aq_solvent_rho: (float) density of solvent (g/L) If ``None``, molar volume/molecular weight is used from xml @@ -255,11 +256,19 @@ class LLEPE: 'function', 'kwargs', and 'independent_params. 'function' is a function of the form - ``function(independent_param__value_list, **kwargs)`` + + ``function(independent_param__value_list, custom_objects_dict, + **kwargs)`` + 'kwargs' are the extra arguments to pass to function + 'independent_params' is a list of parameter names in opt_dict that the dependent_param is a function of. + 'custom_objects_dict' is for accessing the estimator's internal + custom_objects_dict and must be included in the arguments, even if the + custom_objects_dict is not set and is None. + See example code for usage. :param custom_objects_dict: (dict) dictionary containing custom objects format: {: ,...} @@ -883,6 +892,7 @@ class LLEPE: def get_dependant_params_dict(self): """ Returns the dependant_params_dict + :return: dependant_params_dict: (dict) dictionary containing information about parameters dependant on opt_dict """ @@ -891,8 +901,9 @@ class LLEPE: def set_dependant_params_dict(self, dependant_params_dict): """ Sets the dependant_params_dict + :param dependant_params_dict: (dict) dictionary containing information - about parameters dependant on opt_dict + about parameters dependant on opt_dict """ self._dependant_params_dict = dependant_params_dict return None @@ -900,6 +911,7 @@ class LLEPE: def get_custom_objects_dict(self): """ Returns the custom_objects_dict + :return: custom_objects_dict: (dict) dictionary containing information about custom objects from user """ @@ -908,8 +920,9 @@ class LLEPE: def set_custom_objects_dict(self, custom_objects_dict): """ Sets the custom_objects_dict + :param custom_objects_dict: (dict) dictionary containing information - about about custom objects from user + about about custom objects from user """ self._custom_objects_dict = custom_objects_dict return None @@ -1198,9 +1211,11 @@ class LLEPE: def update_custom_objects_dict(self, info_dict): """ updates internal custom_objects_dict with info_dict + :param info_dict: Requires an identical structure to opt_dict Ignores items with keys containing "custom_object_name" - :return: None. + + :return: None """ custom_objects_dict = copy.deepcopy(self._custom_objects_dict) for key in list(info_dict.keys()):