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LLEPE
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removed 'r' when accessing package files

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pull/1/head
titusquah 5 years ago
parent 18ba8dda20
commit 511472d2c4
3 changed files with 28 additions and 20 deletions
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22
.idea/workspace.xml
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@ -3,6 +3,8 @@
<component name="ChangeListManager"> <component name="ChangeListManager">
<list default="true" id="f4439dc0-6756-4612-8f7d-596d8949f300" name="Default Changelist" comment=""> <list default="true" id="f4439dc0-6756-4612-8f7d-596d8949f300" name="Default Changelist" comment="">
<change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" /> <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
<change beforePath="$PROJECT_DIR$/docs/Examples/iterative_fitter.py" beforeDir="false" afterPath="$PROJECT_DIR$/docs/Examples/iterative_fitter.py" afterDir="false" />
<change beforePath="$PROJECT_DIR$/llepe/llepe.py" beforeDir="false" afterPath="$PROJECT_DIR$/llepe/llepe.py" afterDir="false" />
</list> </list>
<option name="SHOW_DIALOG" value="false" /> <option name="SHOW_DIALOG" value="false" />
<option name="HIGHLIGHT_CONFLICTS" value="true" /> <option name="HIGHLIGHT_CONFLICTS" value="true" />
@ -279,7 +281,14 @@
<option name="project" value="LOCAL" /> <option name="project" value="LOCAL" />
<updated>1594768804938</updated> <updated>1594768804938</updated>
</task> </task>
<option name="localTasksCounter" value="17" /> <task id="LOCAL-00017" summary="updated zeroes_removed_PC88A_HCL_NdPrCeLaDySmY.csv to be labeled">
<created>1594769933314</created>
<option name="number" value="00017" />
<option name="presentableId" value="LOCAL-00017" />
<option name="project" value="LOCAL" />
<updated>1594769933314</updated>
</task>
<option name="localTasksCounter" value="18" />
<servers /> <servers />
</component> </component>
<component name="Vcs.Log.Tabs.Properties"> <component name="Vcs.Log.Tabs.Properties">
@ -306,7 +315,8 @@
<MESSAGE value="added example file to do iterative optimization" /> <MESSAGE value="added example file to do iterative optimization" />
<MESSAGE value="commented out skopt in optimizers" /> <MESSAGE value="commented out skopt in optimizers" />
<MESSAGE value="changed xml_path in iterative_fitter.py and added iterative_fitter_monitor.py" /> <MESSAGE value="changed xml_path in iterative_fitter.py and added iterative_fitter_monitor.py" />
<option name="LAST_COMMIT_MESSAGE" value="changed xml_path in iterative_fitter.py and added iterative_fitter_monitor.py" /> <MESSAGE value="updated zeroes_removed_PC88A_HCL_NdPrCeLaDySmY.csv to be labeled" />
<option name="LAST_COMMIT_MESSAGE" value="updated zeroes_removed_PC88A_HCL_NdPrCeLaDySmY.csv to be labeled" />
</component> </component>
<component name="WindowStateProjectService"> <component name="WindowStateProjectService">
<state x="-1330" y="212" key="#Inspections" timestamp="1590787654691"> <state x="-1330" y="212" key="#Inspections" timestamp="1590787654691">
@ -326,11 +336,11 @@
<screen x="-1920" y="2" width="1920" height="1040" /> <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="-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="169" y="115" key="CommitChangelistDialog2" timestamp="1594768802170"> <state x="836" y="163" key="CommitChangelistDialog2" timestamp="1594770211231">
<screen x="0" y="0" width="1920" height="1040" /> <screen x="0" y="0" width="1920" height="1040" />
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<state x="-1364" y="117" key="CommitChangelistDialog2/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1592321237444" /> <state x="-1364" y="117" key="CommitChangelistDialog2/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1592321237444" />
<state x="169" y="115" key="CommitChangelistDialog2/0.0.1920.1040@0.0.1920.1040" timestamp="1594768802170" /> <state x="836" y="163" key="CommitChangelistDialog2/0.0.1920.1040@0.0.1920.1040" timestamp="1594770211231" />
<state x="-1828" y="94" width="1736" height="856" key="DiffContextDialog" timestamp="1591048879404"> <state x="-1828" y="94" width="1736" height="856" key="DiffContextDialog" timestamp="1591048879404">
<screen x="-1920" y="2" width="1920" height="1040" /> <screen x="-1920" y="2" width="1920" height="1040" />
</state> </state>
@ -380,11 +390,11 @@
<screen x="-1920" y="2" width="1920" height="1040" /> <screen x="-1920" y="2" width="1920" height="1040" />
</state> </state>
<state x="-1245" y="438" width="437" height="168" key="VCS.ChangelistChooser/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1592321346068" /> <state x="-1245" y="438" width="437" height="168" key="VCS.ChangelistChooser/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1592321346068" />
<state x="552" y="254" key="Vcs.Push.Dialog.v2" timestamp="1594768807982"> <state x="552" y="254" key="Vcs.Push.Dialog.v2" timestamp="1594769935600">
<screen x="0" y="0" width="1920" height="1040" /> <screen x="0" y="0" width="1920" height="1040" />
</state> </state>
<state x="-1368" y="256" key="Vcs.Push.Dialog.v2/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1592321242949" /> <state x="-1368" y="256" key="Vcs.Push.Dialog.v2/0.0.1536.824/-1920.2.1920.1040@-1920.2.1920.1040" timestamp="1592321242949" />
<state x="552" y="254" key="Vcs.Push.Dialog.v2/0.0.1920.1040@0.0.1920.1040" timestamp="1594768807982" /> <state x="552" y="254" key="Vcs.Push.Dialog.v2/0.0.1920.1040@0.0.1920.1040" timestamp="1594769935600" />
<state x="263" y="182" width="1283" height="717" key="com.intellij.ide.util.TipDialog" timestamp="1594694030135"> <state x="263" y="182" width="1283" height="717" key="com.intellij.ide.util.TipDialog" timestamp="1594694030135">
<screen x="0" y="0" width="1920" height="1040" /> <screen x="0" y="0" width="1920" height="1040" />
</state> </state>

18
docs/Examples/iterative_fitter.py
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@ -15,7 +15,7 @@ meas_pitzer_param_df = pd.read_csv("../../data/csvs/may_pitzer_params.csv")
labeled_data = pd.read_csv("../../data/csvs/" labeled_data = pd.read_csv("../../data/csvs/"
"zeroes_removed_PC88A_HCL_NdPrCeLaDySmY.csv") "zeroes_removed_PC88A_HCL_NdPrCeLaDySmY.csv")
exp_data = labeled_data.drop(labeled_data.columns[0], axis=1) exp_data = labeled_data.drop(labeled_data.columns[0], axis=1)
xml_file = "../../data/xmls/PC88A_HCL_NdPrCeLaDySmY_w_pitzer.xml" xml_file = "PC88A_HCL_NdPrCeLaDySmY_w_pitzer.xml"
eps = 1e-4 eps = 1e-4
mini_eps = 1e-8 mini_eps = 1e-8
x_guesses = [[-5178500.0, -1459500.0], x_guesses = [[-5178500.0, -1459500.0],
@ -103,8 +103,10 @@ while rel_diff > 1e-4:
'aq_solvent_name': 'H2O(L)', 'aq_solvent_name': 'H2O(L)',
'extractant_name': '(HA)2(org)', 'extractant_name': '(HA)2(org)',
'diluant_name': 'dodecane', 'diluant_name': 'dodecane',
'complex_names': ['{0}(H(A)2)3(org)'.format(species)], 'complex_names': ['{0}(H(A)2)3(org)'.format(species)
'extracted_species_ion_names': ['{0}+++'.format(species)], for species in species_list],
'extracted_species_ion_names': ['{0}+++'.format(species)
for species in species_list],
'aq_solvent_rho': 1000.0, 'aq_solvent_rho': 1000.0,
'extractant_rho': 960.0, 'extractant_rho': 960.0,
'diluant_rho': 750.0, 'diluant_rho': 750.0,
@ -172,8 +174,8 @@ while rel_diff > 1e-4:
pitzer_guess_dict[pitzer_param].append(value) pitzer_guess_dict[pitzer_param].append(value)
if i > 2: if i > 2:
mini_rel_diff1 = np.abs(value_list[-1] mini_rel_diff1 = np.abs(value_list[-1]
- value_list[-2])/( - value_list[-2]) / (
np.abs(value_list[-2])) np.abs(value_list[-2]))
mini_rel_diff2 = np.abs(value_list[-2] - value_list[-3]) / ( mini_rel_diff2 = np.abs(value_list[-2] - value_list[-3]) / (
np.abs(value_list[-3])) np.abs(value_list[-3]))
if mini_rel_diff1 < mini_eps and mini_rel_diff2 < mini_eps: if mini_rel_diff1 < mini_eps and mini_rel_diff2 < mini_eps:
@ -184,11 +186,7 @@ while rel_diff > 1e-4:
output_df = pd.DataFrame(output_dict) output_df = pd.DataFrame(output_dict)
old_row = output_df.iloc[-2, :].values[3:] old_row = output_df.iloc[-2, :].values[3:]
new_row = output_df.iloc[-1, :].values[3:] new_row = output_df.iloc[-1, :].values[3:]
rel_diff = np.sum(np.abs(new_row - old_row)/np.abs(old_row)) rel_diff = np.sum(np.abs(new_row - old_row) / np.abs(old_row))
output_dict['rel_diff'].append(rel_diff) output_dict['rel_diff'].append(rel_diff)
output_df = pd.DataFrame(output_dict) output_df = pd.DataFrame(output_dict)
output_df.to_csv('outputs/iterative_fitter_output_df.csv') output_df.to_csv('outputs/iterative_fitter_output_df.csv')

8
llepe/llepe.py
Unescape View File

@ -316,7 +316,7 @@ class LLEPE:
except FileNotFoundError: except FileNotFoundError:
self._phases_xml_filename = \ self._phases_xml_filename = \
pkg_resources.resource_filename('llepe', pkg_resources.resource_filename('llepe',
r'..\data\xmls\{0}'.format( '..\data\xmls\{0}'.format(
phases_xml_filename)) phases_xml_filename))
shutil.copyfile(self._phases_xml_filename, shutil.copyfile(self._phases_xml_filename,
self._temp_xml_file_path) self._temp_xml_file_path)
@ -327,7 +327,7 @@ class LLEPE:
self._exp_df = pd.read_csv(self._exp_data) self._exp_df = pd.read_csv(self._exp_data)
except FileNotFoundError: except FileNotFoundError:
self._exp_data = pkg_resources.resource_filename( 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) self._exp_df = pd.read_csv(self._exp_data)
else: else:
self._exp_df = self._exp_data.copy() self._exp_df = self._exp_data.copy()
@ -442,7 +442,7 @@ class LLEPE:
self._exp_df = pd.read_csv(self._exp_data) self._exp_df = pd.read_csv(self._exp_data)
except FileNotFoundError: except FileNotFoundError:
self._exp_data = pkg_resources.resource_filename( 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) self._exp_df = pd.read_csv(self._exp_data)
else: else:
self._exp_df = exp_data.copy() self._exp_df = exp_data.copy()
@ -496,7 +496,7 @@ class LLEPE:
except FileNotFoundError: except FileNotFoundError:
self._phases_xml_filename = \ self._phases_xml_filename = \
pkg_resources.resource_filename('llepe', pkg_resources.resource_filename('llepe',
r'..\data\xmls\{0}'.format( '..\data\xmls\{0}'.format(
phases_xml_filename)) phases_xml_filename))
shutil.copyfile(self._phases_xml_filename, shutil.copyfile(self._phases_xml_filename,
self._temp_xml_file_path) self._temp_xml_file_path)

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