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diff --git a/ComputeTurbulentViscosity_8cpp.html b/ComputeTurbulentViscosity_8cpp.html
diff --git a/DiffusionSrcForState__N_8cpp.html b/DiffusionSrcForState__N_8cpp.html
@@ -882,12 +882,12 @@ <h2 class="memtitle"><span class="permalink"><a href="#ae2f29294ba4e0edf0c7806af
 <div class="ttc" id="astructDiffChoice_html_a7013ac6c12a0fab52b3c212457441517"><div class="ttname"><a href="structDiffChoice.html#a7013ac6c12a0fab52b3c212457441517">DiffChoice::alpha_T</a></div><div class="ttdeci">amrex::Real alpha_T</div><div class="ttdef"><b>Definition:</b> DiffStruct.H:79</div></div>
 <div class="ttc" id="astructDiffChoice_html_a9a4435111bba7cde59e3187e4ea85d6d"><div class="ttname"><a href="structDiffChoice.html#a9a4435111bba7cde59e3187e4ea85d6d">DiffChoice::alpha_C</a></div><div class="ttdeci">amrex::Real alpha_C</div><div class="ttdef"><b>Definition:</b> DiffStruct.H:80</div></div>
 <div class="ttc" id="astructDiffChoice_html_aed5c75ec58e358a735d97869147b2baf"><div class="ttname"><a href="structDiffChoice.html#aed5c75ec58e358a735d97869147b2baf">DiffChoice::molec_diff_type</a></div><div class="ttdeci">MolecDiffType molec_diff_type</div><div class="ttdef"><b>Definition:</b> DiffStruct.H:76</div></div>
-<div class="ttc" id="astructTurbChoice_html_a0da945128af7536d9fd82586a853de70"><div class="ttname"><a href="structTurbChoice.html#a0da945128af7536d9fd82586a853de70">TurbChoice::advect_QKE</a></div><div class="ttdeci">bool advect_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:305</div></div>
-<div class="ttc" id="astructTurbChoice_html_a15b9bb58cde72bab3f5714934125f3f9"><div class="ttname"><a href="structTurbChoice.html#a15b9bb58cde72bab3f5714934125f3f9">TurbChoice::pbl_type</a></div><div class="ttdeci">PBLType pbl_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:283</div></div>
-<div class="ttc" id="astructTurbChoice_html_a81d6903354abbc64e7dc12b7da91070b"><div class="ttname"><a href="structTurbChoice.html#a81d6903354abbc64e7dc12b7da91070b">TurbChoice::use_QKE</a></div><div class="ttdeci">bool use_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:303</div></div>
-<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:260</div></div>
-<div class="ttc" id="astructTurbChoice_html_ac8533193bb1789d8713f156443ac6801"><div class="ttname"><a href="structTurbChoice.html#ac8533193bb1789d8713f156443ac6801">TurbChoice::pbl_mynn_B1</a></div><div class="ttdeci">amrex::Real pbl_mynn_B1</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:287</div></div>
-<div class="ttc" id="astructTurbChoice_html_aeb3c184b540858407426a606327fba3a"><div class="ttname"><a href="structTurbChoice.html#aeb3c184b540858407426a606327fba3a">TurbChoice::theta_ref</a></div><div class="ttdeci">amrex::Real theta_ref</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:280</div></div>
+<div class="ttc" id="astructTurbChoice_html_a0da945128af7536d9fd82586a853de70"><div class="ttname"><a href="structTurbChoice.html#a0da945128af7536d9fd82586a853de70">TurbChoice::advect_QKE</a></div><div class="ttdeci">bool advect_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:320</div></div>
+<div class="ttc" id="astructTurbChoice_html_a15b9bb58cde72bab3f5714934125f3f9"><div class="ttname"><a href="structTurbChoice.html#a15b9bb58cde72bab3f5714934125f3f9">TurbChoice::pbl_type</a></div><div class="ttdeci">PBLType pbl_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:298</div></div>
+<div class="ttc" id="astructTurbChoice_html_a81d6903354abbc64e7dc12b7da91070b"><div class="ttname"><a href="structTurbChoice.html#a81d6903354abbc64e7dc12b7da91070b">TurbChoice::use_QKE</a></div><div class="ttdeci">bool use_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:318</div></div>
+<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:275</div></div>
+<div class="ttc" id="astructTurbChoice_html_ac8533193bb1789d8713f156443ac6801"><div class="ttname"><a href="structTurbChoice.html#ac8533193bb1789d8713f156443ac6801">TurbChoice::pbl_mynn_B1</a></div><div class="ttdeci">amrex::Real pbl_mynn_B1</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:302</div></div>
+<div class="ttc" id="astructTurbChoice_html_aeb3c184b540858407426a606327fba3a"><div class="ttname"><a href="structTurbChoice.html#aeb3c184b540858407426a606327fba3a">TurbChoice::theta_ref</a></div><div class="ttdeci">amrex::Real theta_ref</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:295</div></div>
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diff --git a/DiffusionSrcForState__T_8cpp.html b/DiffusionSrcForState__T_8cpp.html
@@ -1034,12 +1034,12 @@ <h2 class="memtitle"><span class="permalink"><a href="#a83e088493f24d2c2cad02b63
 <div class="ttc" id="astructDiffChoice_html_a7013ac6c12a0fab52b3c212457441517"><div class="ttname"><a href="structDiffChoice.html#a7013ac6c12a0fab52b3c212457441517">DiffChoice::alpha_T</a></div><div class="ttdeci">amrex::Real alpha_T</div><div class="ttdef"><b>Definition:</b> DiffStruct.H:79</div></div>
 <div class="ttc" id="astructDiffChoice_html_a9a4435111bba7cde59e3187e4ea85d6d"><div class="ttname"><a href="structDiffChoice.html#a9a4435111bba7cde59e3187e4ea85d6d">DiffChoice::alpha_C</a></div><div class="ttdeci">amrex::Real alpha_C</div><div class="ttdef"><b>Definition:</b> DiffStruct.H:80</div></div>
 <div class="ttc" id="astructDiffChoice_html_aed5c75ec58e358a735d97869147b2baf"><div class="ttname"><a href="structDiffChoice.html#aed5c75ec58e358a735d97869147b2baf">DiffChoice::molec_diff_type</a></div><div class="ttdeci">MolecDiffType molec_diff_type</div><div class="ttdef"><b>Definition:</b> DiffStruct.H:76</div></div>
-<div class="ttc" id="astructTurbChoice_html_a0da945128af7536d9fd82586a853de70"><div class="ttname"><a href="structTurbChoice.html#a0da945128af7536d9fd82586a853de70">TurbChoice::advect_QKE</a></div><div class="ttdeci">bool advect_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:305</div></div>
-<div class="ttc" id="astructTurbChoice_html_a15b9bb58cde72bab3f5714934125f3f9"><div class="ttname"><a href="structTurbChoice.html#a15b9bb58cde72bab3f5714934125f3f9">TurbChoice::pbl_type</a></div><div class="ttdeci">PBLType pbl_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:283</div></div>
-<div class="ttc" id="astructTurbChoice_html_a81d6903354abbc64e7dc12b7da91070b"><div class="ttname"><a href="structTurbChoice.html#a81d6903354abbc64e7dc12b7da91070b">TurbChoice::use_QKE</a></div><div class="ttdeci">bool use_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:303</div></div>
-<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:260</div></div>
-<div class="ttc" id="astructTurbChoice_html_ac8533193bb1789d8713f156443ac6801"><div class="ttname"><a href="structTurbChoice.html#ac8533193bb1789d8713f156443ac6801">TurbChoice::pbl_mynn_B1</a></div><div class="ttdeci">amrex::Real pbl_mynn_B1</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:287</div></div>
-<div class="ttc" id="astructTurbChoice_html_aeb3c184b540858407426a606327fba3a"><div class="ttname"><a href="structTurbChoice.html#aeb3c184b540858407426a606327fba3a">TurbChoice::theta_ref</a></div><div class="ttdeci">amrex::Real theta_ref</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:280</div></div>
+<div class="ttc" id="astructTurbChoice_html_a0da945128af7536d9fd82586a853de70"><div class="ttname"><a href="structTurbChoice.html#a0da945128af7536d9fd82586a853de70">TurbChoice::advect_QKE</a></div><div class="ttdeci">bool advect_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:320</div></div>
+<div class="ttc" id="astructTurbChoice_html_a15b9bb58cde72bab3f5714934125f3f9"><div class="ttname"><a href="structTurbChoice.html#a15b9bb58cde72bab3f5714934125f3f9">TurbChoice::pbl_type</a></div><div class="ttdeci">PBLType pbl_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:298</div></div>
+<div class="ttc" id="astructTurbChoice_html_a81d6903354abbc64e7dc12b7da91070b"><div class="ttname"><a href="structTurbChoice.html#a81d6903354abbc64e7dc12b7da91070b">TurbChoice::use_QKE</a></div><div class="ttdeci">bool use_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:318</div></div>
+<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:275</div></div>
+<div class="ttc" id="astructTurbChoice_html_ac8533193bb1789d8713f156443ac6801"><div class="ttname"><a href="structTurbChoice.html#ac8533193bb1789d8713f156443ac6801">TurbChoice::pbl_mynn_B1</a></div><div class="ttdeci">amrex::Real pbl_mynn_B1</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:302</div></div>
+<div class="ttc" id="astructTurbChoice_html_aeb3c184b540858407426a606327fba3a"><div class="ttname"><a href="structTurbChoice.html#aeb3c184b540858407426a606327fba3a">TurbChoice::theta_ref</a></div><div class="ttdeci">amrex::Real theta_ref</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:295</div></div>
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diff --git a/ERF__make__sources_8cpp.html b/ERF__make__sources_8cpp.html
@@ -622,9 +622,9 @@ <h2 class="memtitle"><span class="permalink"><a href="#ae5ce4675f35ecdefeb8d33f1
 <div class="ttc" id="astructSolverChoice_html_afdd906d035384fd962efab24e7a6da7c"><div class="ttname"><a href="structSolverChoice.html#afdd906d035384fd962efab24e7a6da7c">SolverChoice::ave_plane</a></div><div class="ttdeci">int ave_plane</div><div class="ttdef"><b>Definition:</b> DataStruct.H:557</div></div>
 <div class="ttc" id="astructSpongeChoice_html_a1a41f754595d713df32583f0b0fa606e"><div class="ttname"><a href="structSpongeChoice.html#a1a41f754595d713df32583f0b0fa606e">SpongeChoice::sponge_type</a></div><div class="ttdeci">std::string sponge_type</div><div class="ttdef"><b>Definition:</b> SpongeStruct.H:61</div></div>
 <div class="ttc" id="astructTurbChoice_html"><div class="ttname"><a href="structTurbChoice.html">TurbChoice</a></div><div class="ttdef"><b>Definition:</b> TurbStruct.H:16</div></div>
-<div class="ttc" id="astructTurbChoice_html_a0da945128af7536d9fd82586a853de70"><div class="ttname"><a href="structTurbChoice.html#a0da945128af7536d9fd82586a853de70">TurbChoice::advect_QKE</a></div><div class="ttdeci">bool advect_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:305</div></div>
-<div class="ttc" id="astructTurbChoice_html_a81d6903354abbc64e7dc12b7da91070b"><div class="ttname"><a href="structTurbChoice.html#a81d6903354abbc64e7dc12b7da91070b">TurbChoice::use_QKE</a></div><div class="ttdeci">bool use_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:303</div></div>
-<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:260</div></div>
+<div class="ttc" id="astructTurbChoice_html_a0da945128af7536d9fd82586a853de70"><div class="ttname"><a href="structTurbChoice.html#a0da945128af7536d9fd82586a853de70">TurbChoice::advect_QKE</a></div><div class="ttdeci">bool advect_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:320</div></div>
+<div class="ttc" id="astructTurbChoice_html_a81d6903354abbc64e7dc12b7da91070b"><div class="ttname"><a href="structTurbChoice.html#a81d6903354abbc64e7dc12b7da91070b">TurbChoice::use_QKE</a></div><div class="ttdeci">bool use_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:318</div></div>
+<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:275</div></div>
 <div class="ttc" id="astructTurbulentPerturbation_html_a6c1c35c60d8c8a7e66c770d78fb314ef"><div class="ttname"><a href="structTurbulentPerturbation.html#a6c1c35c60d8c8a7e66c770d78fb314ef">TurbulentPerturbation::pb_cell</a></div><div class="ttdeci">amrex::MultiFab pb_cell</div><div class="ttdef"><b>Definition:</b> TurbPertStruct.H:525</div></div>
 <div class="ttc" id="astructTurbulentPerturbation_html_adcb414231654ad9f5232a1a3377c30f2"><div class="ttname"><a href="structTurbulentPerturbation.html#adcb414231654ad9f5232a1a3377c30f2">TurbulentPerturbation::apply_tpi</a></div><div class="ttdeci">void apply_tpi(const int &amp;lev, const amrex::Box &amp;vbx, const int &amp;comp, const amrex::IndexType &amp;m_ixtype, const amrex::Array4&lt; amrex::Real &gt; &amp;src_arr, const amrex::Array4&lt; amrex::Real const &gt; &amp;pert_cell)</div><div class="ttdef"><b>Definition:</b> TurbPertStruct.H:243</div></div>
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diff --git a/ERF__make__tau__terms_8cpp.html b/ERF__make__tau__terms_8cpp.html
@@ -747,8 +747,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#aeb0929ca1a4b2e5eb9719d51
 <div class="ttc" id="astructSolverChoice_html_aa53b017d79e0067923180a0aa59367b4"><div class="ttname"><a href="structSolverChoice.html#aa53b017d79e0067923180a0aa59367b4">SolverChoice::turbChoice</a></div><div class="ttdeci">amrex::Vector&lt; TurbChoice &gt; turbChoice</div><div class="ttdef"><b>Definition:</b> DataStruct.H:469</div></div>
 <div class="ttc" id="astructSolverChoice_html_ab734eb0a5147b93dc6590038b6decc60"><div class="ttname"><a href="structSolverChoice.html#ab734eb0a5147b93dc6590038b6decc60">SolverChoice::terrain_type</a></div><div class="ttdeci">TerrainType terrain_type</div><div class="ttdef"><b>Definition:</b> DataStruct.H:545</div></div>
 <div class="ttc" id="astructTurbChoice_html"><div class="ttname"><a href="structTurbChoice.html">TurbChoice</a></div><div class="ttdef"><b>Definition:</b> TurbStruct.H:16</div></div>
-<div class="ttc" id="astructTurbChoice_html_a15b9bb58cde72bab3f5714934125f3f9"><div class="ttname"><a href="structTurbChoice.html#a15b9bb58cde72bab3f5714934125f3f9">TurbChoice::pbl_type</a></div><div class="ttdeci">PBLType pbl_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:283</div></div>
-<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:260</div></div>
+<div class="ttc" id="astructTurbChoice_html_a15b9bb58cde72bab3f5714934125f3f9"><div class="ttname"><a href="structTurbChoice.html#a15b9bb58cde72bab3f5714934125f3f9">TurbChoice::pbl_type</a></div><div class="ttdeci">PBLType pbl_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:298</div></div>
+<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:275</div></div>
 </div><!-- fragment -->
 <p class="reference">Referenced by <a class="el" href="ERF__slow__rhs__pre_8cpp.html#ad018745b333f31583ebb5940d370ea6b">erf_slow_rhs_pre()</a>.</p>
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diff --git a/ERF__slow__rhs__post_8cpp.html b/ERF__slow__rhs__post_8cpp.html
@@ -891,10 +891,10 @@ <h2 class="memtitle"><span class="permalink"><a href="#aac3319866aabf87a68fb81ce
 <div class="ttc" id="astructSolverChoice_html_ad77ddc1a1eff7c49195d54b69aab46f5"><div class="ttname"><a href="structSolverChoice.html#ad77ddc1a1eff7c49195d54b69aab46f5">SolverChoice::incompressible</a></div><div class="ttdeci">amrex::Vector&lt; int &gt; incompressible</div><div class="ttdef"><b>Definition:</b> DataStruct.H:477</div></div>
 <div class="ttc" id="astructSolverChoice_html_af976afa61859c07e6249963edc367c2d"><div class="ttname"><a href="structSolverChoice.html#af976afa61859c07e6249963edc367c2d">SolverChoice::coupling_type</a></div><div class="ttdeci">CouplingType coupling_type</div><div class="ttdef"><b>Definition:</b> DataStruct.H:544</div></div>
 <div class="ttc" id="astructTurbChoice_html"><div class="ttname"><a href="structTurbChoice.html">TurbChoice</a></div><div class="ttdef"><b>Definition:</b> TurbStruct.H:16</div></div>
-<div class="ttc" id="astructTurbChoice_html_a0da945128af7536d9fd82586a853de70"><div class="ttname"><a href="structTurbChoice.html#a0da945128af7536d9fd82586a853de70">TurbChoice::advect_QKE</a></div><div class="ttdeci">bool advect_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:305</div></div>
-<div class="ttc" id="astructTurbChoice_html_a15b9bb58cde72bab3f5714934125f3f9"><div class="ttname"><a href="structTurbChoice.html#a15b9bb58cde72bab3f5714934125f3f9">TurbChoice::pbl_type</a></div><div class="ttdeci">PBLType pbl_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:283</div></div>
-<div class="ttc" id="astructTurbChoice_html_a81d6903354abbc64e7dc12b7da91070b"><div class="ttname"><a href="structTurbChoice.html#a81d6903354abbc64e7dc12b7da91070b">TurbChoice::use_QKE</a></div><div class="ttdeci">bool use_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:303</div></div>
-<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:260</div></div>
+<div class="ttc" id="astructTurbChoice_html_a0da945128af7536d9fd82586a853de70"><div class="ttname"><a href="structTurbChoice.html#a0da945128af7536d9fd82586a853de70">TurbChoice::advect_QKE</a></div><div class="ttdeci">bool advect_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:320</div></div>
+<div class="ttc" id="astructTurbChoice_html_a15b9bb58cde72bab3f5714934125f3f9"><div class="ttname"><a href="structTurbChoice.html#a15b9bb58cde72bab3f5714934125f3f9">TurbChoice::pbl_type</a></div><div class="ttdeci">PBLType pbl_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:298</div></div>
+<div class="ttc" id="astructTurbChoice_html_a81d6903354abbc64e7dc12b7da91070b"><div class="ttname"><a href="structTurbChoice.html#a81d6903354abbc64e7dc12b7da91070b">TurbChoice::use_QKE</a></div><div class="ttdeci">bool use_QKE</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:318</div></div>
+<div class="ttc" id="astructTurbChoice_html_abbba68e0d699dd97701d31a0e37d5304"><div class="ttname"><a href="structTurbChoice.html#abbba68e0d699dd97701d31a0e37d5304">TurbChoice::les_type</a></div><div class="ttdeci">LESType les_type</div><div class="ttdef"><b>Definition:</b> TurbStruct.H:275</div></div>
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