Modified reeps to grab charge from REE in xml file for initial chlorine moles calculation

.idea/dictionaries/Titus.xml

@@ -7,6 +7,7 @@
       <w>equilibrate</w>
       <w>extractant</w>
       <w>kmol</w>
+      <w>lmse</w>
       <w>ndarray</w>
       <w>pred</w>
       <w>reeps</w>

.idea/workspace.xml

@@ -2,11 +2,11 @@
 <project version="4">
   <component name="ChangeListManager">
     <list default="true" id="f4439dc0-6756-4612-8f7d-596d8949f300" name="Default Changelist" comment="">
-      <change afterPath="$PROJECT_DIR$/data/xmls/elementz.xml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/.idea/dictionaries/Titus.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/dictionaries/Titus.xml" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/data/xmls/twophase.xml" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/tests/one_comp_settings.txt" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/data/xmls/twophase.xml" beforeDir="false" afterPath="$PROJECT_DIR$/data/xmls/twophase.xml" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/reeps.py" beforeDir="false" afterPath="$PROJECT_DIR$/reeps.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/tests/one_comp_settings.txt" beforeDir="false" />
       <change beforePath="$PROJECT_DIR$/tests/test_reeps.py" beforeDir="false" afterPath="$PROJECT_DIR$/tests/test_reeps.py" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
@@ -37,20 +37,17 @@
     <property name="run.code.analysis.last.selected.profile" value="aDefault" />
     <property name="settings.editor.selected.configurable" value="com.jetbrains.python.configuration.PyActiveSdkModuleConfigurable" />
   </component>
-  <component name="RunManager" selected="Python.test">
+  <component name="RunManager" selected="Python.test_reeps">
-    <configuration name="fit" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
+    <configuration name="surfmethods" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
       <module name="parameter-estimation" />
       <option name="INTERPRETER_OPTIONS" value="" />
       <option name="PARENT_ENVS" value="true" />
-      <envs>
-        <env name="PYTHONUNBUFFERED" value="1" />
-      </envs>
       <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/../../parameter estimation/parameter estimation" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/../../anl_box/Box Sync/titus/onboarding/codes/multi/1_fit/01_Surface/1_Nd" />
       <option name="IS_MODULE_SDK" value="false" />
       <option name="ADD_CONTENT_ROOTS" value="true" />
       <option name="ADD_SOURCE_ROOTS" value="true" />
-      <option name="SCRIPT_NAME" value="$PROJECT_DIR$/../../parameter estimation/parameter estimation/fit.py" />
+      <option name="SCRIPT_NAME" value="$PROJECT_DIR$/../../anl_box/Box Sync/titus/onboarding/codes/multi/1_fit/01_Surface/1_Nd/surfmethods.py" />
       <option name="PARAMETERS" value="" />
       <option name="SHOW_COMMAND_LINE" value="true" />
       <option name="EMULATE_TERMINAL" value="false" />
@@ -63,6 +60,9 @@
       <module name="parameter-estimation" />
       <option name="INTERPRETER_OPTIONS" value="" />
       <option name="PARENT_ENVS" value="true" />
+      <envs>
+        <env name="PYTHONUNBUFFERED" value="1" />
+      </envs>
       <option name="SDK_HOME" value="" />
       <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/../../parameter estimation/parameter estimation" />
       <option name="IS_MODULE_SDK" value="false" />
@@ -132,7 +132,7 @@
     </configuration>
     <recent_temporary>
       <list>
-        <item itemvalue="Python.test" />
+        <item itemvalue="Python.test_reeps" />
         <item itemvalue="Python.test_reeps" />
         <item itemvalue="Python.test_reeps" />
         <item itemvalue="Python.test_reeps" />
@@ -208,7 +208,14 @@
       <option name="project" value="LOCAL" />
       <updated>1591119253733</updated>
     </task>
-    <option name="localTasksCounter" value="7" />
+    <task id="LOCAL-00007" summary="Modified reeps to grab charge from REE in xml file for initial chlorine moles calculation">
+      <created>1591130305884</created>
+      <option name="number" value="00007" />
+      <option name="presentableId" value="LOCAL-00007" />
+      <option name="project" value="LOCAL" />
+      <updated>1591130305884</updated>
+    </task>
+    <option name="localTasksCounter" value="8" />
     <servers />
   </component>
   <component name="Vcs.Log.Tabs.Properties">
@@ -227,7 +234,8 @@
   <component name="VcsManagerConfiguration">
     <MESSAGE value="started project" />
     <MESSAGE value="Completed one composition parameter estimation" />
-    <option name="LAST_COMMIT_MESSAGE" value="Completed one composition parameter estimation" />
+    <MESSAGE value="Modified reeps to grab charge from REE in xml file for initial chlorine moles calculation" />
+    <option name="LAST_COMMIT_MESSAGE" value="Modified reeps to grab charge from REE in xml file for initial chlorine moles calculation" />
   </component>
   <component name="WindowStateProjectService">
     <state x="-1330" y="212" key="#Inspections" timestamp="1590787654691">
@@ -246,10 +254,10 @@
       <screen x="-1920" y="2" width="1920" height="1040" />
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     <state x="-1213" y="379" key="ANALYSIS_DLG_com.intellij.analysis.BaseAnalysisAction$1/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1590787657711" />
-    <state x="-1364" y="117" key="CommitChangelistDialog2" timestamp="1591119252191">
+    <state x="-1364" y="117" key="CommitChangelistDialog2" timestamp="1591130304224">
       <screen x="-1920" y="2" width="1920" height="1040" />
     </state>
-    <state x="-1364" y="117" key="CommitChangelistDialog2/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1591119252191" />
+    <state x="-1364" y="117" key="CommitChangelistDialog2/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1591130304224" />
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       <screen x="-1920" y="2" width="1920" height="1040" />
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@@ -290,10 +298,10 @@
       <screen x="-1920" y="2" width="1920" height="1040" />
     </state>
     <state x="-1368" y="256" key="Vcs.Push.Dialog.v2/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1591047662716" />
-    <state x="-1341" y="300" key="com.intellij.ide.util.TipDialog" timestamp="1591116828596">
+    <state x="-1341" y="300" key="com.intellij.ide.util.TipDialog" timestamp="1591192469960">
       <screen x="-1920" y="2" width="1920" height="1040" />
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+    <state x="-1341" y="300" key="com.intellij.ide.util.TipDialog/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1591192469960" />
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data/xmls/twophase.xml

@@ -50,7 +50,7 @@
         <const_cp Tmax="300.0" Tmin="298.0">
            <t0 units="K">298.14999999999998</t0>
 	    
-	   <h0 units="J/mol" updated="Updated at 18:24:54">-4848809.807683906</h0> 
+	   <h0 units="J/mol" updated="Updated at 11:29 6-3-2020">-4704703.645715787</h0> 
 	   <s0 units="J/mol/K"> 1117.965 </s0>  
            <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>

reeps.py

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

tests/one_comp_settings.txt

@@ -1 +0,0 @@
-{"exp_csv_filename": "../data/csvs/exp_data.csv", "phases_xml_filename": "../data/xmls/twophase.xml", "x_guess": 0.96, "h_guess": -4856609000.0, "phase_names": ["HCl_electrolyte", "PC88A_liquid"], "aq_solvent_name": "H2O(L)", "extractant_name": "(HA)2(org)", "diluant_name": "dodecane", "complex_name": "Nd(H(A)2)3(org)", "rare_earth_ion_name": "Nd+++", "aq_solvent_rho": 1000.0, "extractant_rho": 960.0, "diluant_rho": 750.0}

tests/test_reeps.py

@@ -5,8 +5,9 @@ sys.path.append('../')
 from reeps import REEPS
 
 
-with open('one_comp_settings.txt') as file:
+with open('one_ree_settings.txt') as file:
     testing_params = json.load(file)
+
 beaker = REEPS(**testing_params)
 
 minimizer_kwargs = {"method": 'SLSQP',
@@ -15,5 +16,7 @@ minimizer_kwargs = {"method": 'SLSQP',
                     "options": {'disp': True, 'maxiter': 1000, 'ftol': 1e-6}}
 est_enthalpy = beaker.fit(minimizer_kwargs)
 print(est_enthalpy)
+# info_dict = {"Nd(H(A)2)3(org)": {"h0": est_enthalpy}}
+#
 beaker.update_xml(est_enthalpy)
 beaker.parity_plot()