@@ -779,93 +779,94 @@ var NAVTREE =
779779 [ "Testing" , "testing.html" , null ] ,
780780 [ "Thermochemistry implementation" , "thermochemistry.html" , [
781781 [ "Mechanism generation" , "thermochemistry.html#autotoc_md588" , null ] ,
782- [ "Mixing-layer initial conditions" , "thermochemistry.html#autotoc_md589" , null ] ,
783- [ "Validation" , "thermochemistry.html#autotoc_md590" , null ]
782+ [ "Surface chemistry" , "thermochemistry.html#autotoc_md589" , null ] ,
783+ [ "Mixing-layer initial conditions" , "thermochemistry.html#autotoc_md590" , null ] ,
784+ [ "Validation" , "thermochemistry.html#autotoc_md591" , null ]
784785 ] ] ,
785786 [ "Troubleshooting Guide" , "troubleshooting.html" , [
786- [ "Troubleshooting Guide" , "troubleshooting.html#autotoc_md591 " , [
787- [ "Quick Reference" , "troubleshooting.html#autotoc_md592 " , [
788- [ "Debugging Flags" , "troubleshooting.html#autotoc_md593 " , null ] ,
789- [ "Profiling Flags" , "troubleshooting.html#autotoc_md594 " , null ] ,
790- [ "Useful Commands" , "troubleshooting.html#autotoc_md595 " , null ]
791- ] ] ,
792- [ "Debugging Workflow" , "troubleshooting.html#autotoc_md597 " , [
793- [ "Build Fails?" , "troubleshooting.html#autotoc_md598 " , null ] ,
794- [ "Run Fails?" , "troubleshooting.html#autotoc_md599 " , null ] ,
795- [ "Test Fails?" , "troubleshooting.html#autotoc_md600 " , null ]
796- ] ] ,
797- [ "Build Debugging" , "troubleshooting.html#autotoc_md602 " , [
798- [ "Verbosity Levels" , "troubleshooting.html#autotoc_md603 " , null ] ,
799- [ "Debug Builds" , "troubleshooting.html#autotoc_md604 " , null ] ,
800- [ "Code Coverage" , "troubleshooting.html#autotoc_md605 " , null ] ,
801- [ "Isolating Issues" , "troubleshooting.html#autotoc_md606 " , null ] ,
802- [ "Clean Rebuild" , "troubleshooting.html#autotoc_md607 " , null ]
803- ] ] ,
804- [ "Runtime Debugging" , "troubleshooting.html#autotoc_md609 " , [
805- [ "Case Validation" , "troubleshooting.html#autotoc_md610 " , null ] ,
806- [ "Verbose Runs" , "troubleshooting.html#autotoc_md611 " , null ] ,
807- [ "Debug Log" , "troubleshooting.html#autotoc_md612 " , null ] ,
808- [ "Running with Fewer Ranks" , "troubleshooting.html#autotoc_md613 " , null ]
809- ] ] ,
810- [ "Test Debugging" , "troubleshooting.html#autotoc_md615 " , [
811- [ "Running Specific Tests" , "troubleshooting.html#autotoc_md616 " , null ] ,
812- [ "Serial Test Execution" , "troubleshooting.html#autotoc_md617 " , null ] ,
813- [ "Test Output Location" , "troubleshooting.html#autotoc_md618 " , null ] ,
814- [ "Regenerating Golden Files" , "troubleshooting.html#autotoc_md619 " , null ] ,
815- [ "Understanding Test Failures" , "troubleshooting.html#autotoc_md620 " , null ]
816- ] ] ,
817- [ "Performance Profiling" , "troubleshooting.html#autotoc_md622 " , [
818- [ "NVIDIA GPU Profiling" , "troubleshooting.html#autotoc_md623 " , null ] ,
819- [ "AMD GPU Profiling" , "troubleshooting.html#autotoc_md624 " , null ] ,
820- [ "Performance vs Correctness" , "troubleshooting.html#autotoc_md625 " , null ]
821- ] ] ,
822- [ "Common Build Errors" , "troubleshooting.html#autotoc_md627 " , [
823- [ "\"CMake could not find MPI\"" , "troubleshooting.html#autotoc_md628 " , null ] ,
824- [ "\"CMake could not find a Fortran compiler\"" , "troubleshooting.html#autotoc_md629 " , null ] ,
825- [ "\"Fypp preprocessing failed\"" , "troubleshooting.html#autotoc_md630 " , null ] ,
826- [ "Build fails with GPU/OpenACC errors" , "troubleshooting.html#autotoc_md631 " , null ] ,
827- [ "\"Module not found\" on HPC" , "troubleshooting.html#autotoc_md632 " , null ]
828- ] ] ,
829- [ "Common Runtime Errors" , "troubleshooting.html#autotoc_md634 " , [
830- [ "\"Case parameter constraint violations\"" , "troubleshooting.html#autotoc_md635 " , null ] ,
831- [ "\"NaN detected\"" , "troubleshooting.html#autotoc_md636 " , null ] ,
832- [ "GPU not detected" , "troubleshooting.html#autotoc_md637 " , null ] ,
833- [ "MPI errors or hangs" , "troubleshooting.html#autotoc_md638 " , null ]
834- ] ] ,
835- [ "Visualization Issues" , "troubleshooting.html#autotoc_md640 " , [
836- [ "\"No 'binary/' or 'silo_hdf5/' directory found\"" , "troubleshooting.html#autotoc_md641 " , null ] ,
837- [ "\"Variable 'X' not found\"" , "troubleshooting.html#autotoc_md642 " , null ] ,
838- [ "\"h5py is required to read Silo-HDF5 files\"" , "troubleshooting.html#autotoc_md643 " , null ] ,
839- [ "Visualization looks wrong or has artifacts" , "troubleshooting.html#autotoc_md644 " , null ]
840- ] ] ,
841- [ "Getting Help" , "troubleshooting.html#autotoc_md646 " , null ]
787+ [ "Troubleshooting Guide" , "troubleshooting.html#autotoc_md592 " , [
788+ [ "Quick Reference" , "troubleshooting.html#autotoc_md593 " , [
789+ [ "Debugging Flags" , "troubleshooting.html#autotoc_md594 " , null ] ,
790+ [ "Profiling Flags" , "troubleshooting.html#autotoc_md595 " , null ] ,
791+ [ "Useful Commands" , "troubleshooting.html#autotoc_md596 " , null ]
792+ ] ] ,
793+ [ "Debugging Workflow" , "troubleshooting.html#autotoc_md598 " , [
794+ [ "Build Fails?" , "troubleshooting.html#autotoc_md599 " , null ] ,
795+ [ "Run Fails?" , "troubleshooting.html#autotoc_md600 " , null ] ,
796+ [ "Test Fails?" , "troubleshooting.html#autotoc_md601 " , null ]
797+ ] ] ,
798+ [ "Build Debugging" , "troubleshooting.html#autotoc_md603 " , [
799+ [ "Verbosity Levels" , "troubleshooting.html#autotoc_md604 " , null ] ,
800+ [ "Debug Builds" , "troubleshooting.html#autotoc_md605 " , null ] ,
801+ [ "Code Coverage" , "troubleshooting.html#autotoc_md606 " , null ] ,
802+ [ "Isolating Issues" , "troubleshooting.html#autotoc_md607 " , null ] ,
803+ [ "Clean Rebuild" , "troubleshooting.html#autotoc_md608 " , null ]
804+ ] ] ,
805+ [ "Runtime Debugging" , "troubleshooting.html#autotoc_md610 " , [
806+ [ "Case Validation" , "troubleshooting.html#autotoc_md611 " , null ] ,
807+ [ "Verbose Runs" , "troubleshooting.html#autotoc_md612 " , null ] ,
808+ [ "Debug Log" , "troubleshooting.html#autotoc_md613 " , null ] ,
809+ [ "Running with Fewer Ranks" , "troubleshooting.html#autotoc_md614 " , null ]
810+ ] ] ,
811+ [ "Test Debugging" , "troubleshooting.html#autotoc_md616 " , [
812+ [ "Running Specific Tests" , "troubleshooting.html#autotoc_md617 " , null ] ,
813+ [ "Serial Test Execution" , "troubleshooting.html#autotoc_md618 " , null ] ,
814+ [ "Test Output Location" , "troubleshooting.html#autotoc_md619 " , null ] ,
815+ [ "Regenerating Golden Files" , "troubleshooting.html#autotoc_md620 " , null ] ,
816+ [ "Understanding Test Failures" , "troubleshooting.html#autotoc_md621 " , null ]
817+ ] ] ,
818+ [ "Performance Profiling" , "troubleshooting.html#autotoc_md623 " , [
819+ [ "NVIDIA GPU Profiling" , "troubleshooting.html#autotoc_md624 " , null ] ,
820+ [ "AMD GPU Profiling" , "troubleshooting.html#autotoc_md625 " , null ] ,
821+ [ "Performance vs Correctness" , "troubleshooting.html#autotoc_md626 " , null ]
822+ ] ] ,
823+ [ "Common Build Errors" , "troubleshooting.html#autotoc_md628 " , [
824+ [ "\"CMake could not find MPI\"" , "troubleshooting.html#autotoc_md629 " , null ] ,
825+ [ "\"CMake could not find a Fortran compiler\"" , "troubleshooting.html#autotoc_md630 " , null ] ,
826+ [ "\"Fypp preprocessing failed\"" , "troubleshooting.html#autotoc_md631 " , null ] ,
827+ [ "Build fails with GPU/OpenACC errors" , "troubleshooting.html#autotoc_md632 " , null ] ,
828+ [ "\"Module not found\" on HPC" , "troubleshooting.html#autotoc_md633 " , null ]
829+ ] ] ,
830+ [ "Common Runtime Errors" , "troubleshooting.html#autotoc_md635 " , [
831+ [ "\"Case parameter constraint violations\"" , "troubleshooting.html#autotoc_md636 " , null ] ,
832+ [ "\"NaN detected\"" , "troubleshooting.html#autotoc_md637 " , null ] ,
833+ [ "GPU not detected" , "troubleshooting.html#autotoc_md638 " , null ] ,
834+ [ "MPI errors or hangs" , "troubleshooting.html#autotoc_md639 " , null ]
835+ ] ] ,
836+ [ "Visualization Issues" , "troubleshooting.html#autotoc_md641 " , [
837+ [ "\"No 'binary/' or 'silo_hdf5/' directory found\"" , "troubleshooting.html#autotoc_md642 " , null ] ,
838+ [ "\"Variable 'X' not found\"" , "troubleshooting.html#autotoc_md643 " , null ] ,
839+ [ "\"h5py is required to read Silo-HDF5 files\"" , "troubleshooting.html#autotoc_md644 " , null ] ,
840+ [ "Visualization looks wrong or has artifacts" , "troubleshooting.html#autotoc_md645 " , null ]
841+ ] ] ,
842+ [ "Getting Help" , "troubleshooting.html#autotoc_md647 " , null ]
842843 ] ]
843844 ] ] ,
844845 [ "Flow visualization" , "visualization.html" , [
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846- [ "Quick visualization with <span class=\"tt\">./mfc.sh viz</span>" , "visualization.html#autotoc_md649 " , [
847- [ "Basic usage" , "visualization.html#autotoc_md650 " , null ] ,
848- [ "Exploring available data" , "visualization.html#autotoc_md651 " , null ] ,
849- [ "Timestep selection" , "visualization.html#autotoc_md652 " , null ] ,
850- [ "Rendering options" , "visualization.html#autotoc_md653 " , null ] ,
851- [ "3D slicing" , "visualization.html#autotoc_md654 " , null ] ,
852- [ "Video generation" , "visualization.html#autotoc_md655 " , null ] ,
853- [ "Tiled 1D rendering" , "visualization.html#autotoc_md656 " , null ] ,
854- [ "Interactive mode" , "visualization.html#autotoc_md657 " , null ] ,
855- [ "Terminal UI (TUI)" , "visualization.html#autotoc_md658 " , null ] ,
856- [ "Plot styling" , "visualization.html#autotoc_md659 " , null ] ,
857- [ "Format selection" , "visualization.html#autotoc_md660 " , null ] ,
858- [ "Complete option reference" , "visualization.html#autotoc_md661 " , null ]
859- ] ] ,
860- [ "Visualizing with ParaView" , "visualization.html#autotoc_md663 " , [
861- [ "Visualizing data in cylindrical coordinates" , "visualization.html#autotoc_md664 " , null ]
862- ] ] ,
863- [ "Visualizing with VisIt" , "visualization.html#autotoc_md665 " , null ] ,
864- [ "Serial data output" , "visualization.html#autotoc_md666 " , null ] ,
865- [ "Remote Visualization on PACE Phoenix" , "visualization.html#autotoc_md667 " , [
866- [ "Step 1: Setting up your Environment" , "visualization.html#autotoc_md668 " , null ] ,
867- [ "Step 2: Customizing the script" , "visualization.html#autotoc_md669 " , null ] ,
868- [ "Step 3: Running pace-paraview-server" , "visualization.html#autotoc_md670 " , null ]
846+ [ "Flow visualization" , "visualization.html#autotoc_md648 " , [
847+ [ "Quick visualization with <span class=\"tt\">./mfc.sh viz</span>" , "visualization.html#autotoc_md650 " , [
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849+ [ "Exploring available data" , "visualization.html#autotoc_md652 " , null ] ,
850+ [ "Timestep selection" , "visualization.html#autotoc_md653 " , null ] ,
851+ [ "Rendering options" , "visualization.html#autotoc_md654 " , null ] ,
852+ [ "3D slicing" , "visualization.html#autotoc_md655 " , null ] ,
853+ [ "Video generation" , "visualization.html#autotoc_md656 " , null ] ,
854+ [ "Tiled 1D rendering" , "visualization.html#autotoc_md657 " , null ] ,
855+ [ "Interactive mode" , "visualization.html#autotoc_md658 " , null ] ,
856+ [ "Terminal UI (TUI)" , "visualization.html#autotoc_md659 " , null ] ,
857+ [ "Plot styling" , "visualization.html#autotoc_md660 " , null ] ,
858+ [ "Format selection" , "visualization.html#autotoc_md661 " , null ] ,
859+ [ "Complete option reference" , "visualization.html#autotoc_md662 " , null ]
860+ ] ] ,
861+ [ "Visualizing with ParaView" , "visualization.html#autotoc_md664 " , [
862+ [ "Visualizing data in cylindrical coordinates" , "visualization.html#autotoc_md665 " , null ]
863+ ] ] ,
864+ [ "Visualizing with VisIt" , "visualization.html#autotoc_md666 " , null ] ,
865+ [ "Serial data output" , "visualization.html#autotoc_md667 " , null ] ,
866+ [ "Remote Visualization on PACE Phoenix" , "visualization.html#autotoc_md668 " , [
867+ [ "Step 1: Setting up your Environment" , "visualization.html#autotoc_md669 " , null ] ,
868+ [ "Step 2: Customizing the script" , "visualization.html#autotoc_md670 " , null ] ,
869+ [ "Step 3: Running pace-paraview-server" , "visualization.html#autotoc_md671 " , null ]
869870 ] ]
870871 ] ]
871872 ] ] ,
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