JFNK_HO case files updates

papers/JFNK_highOrder/linearElastic/cantilever/Allrun

@@ -7,11 +7,11 @@ source solids4FoamScripts.sh
 solids4Foam::caseDoesNotRunWithFoamExtend
 
 # solids4Foam location path
-export SOLIDS4FOAM_DIR=/Users/ivanbatistic/work/solids4foam-ib-highOrder
+export SOLIDS4FOAM_DIR=/Users/ivanbatistic/work/solids4foam-ib/solids4foam-ib-2412/
 echo "SOLIDS4FOAM_DIR = $SOLIDS4FOAM_DIR"
 
 # Compile the cantileverBeam library
-(cd  analyticalCantilever && ./Allwmake -j -s)
+(cd src && ./Allwmake -j -s)
 
 # Segregated version require a lot of time to converge, I will skip it for
 # now. Tet mesh is not working with snes becouse of gradient at corner cells
@@ -22,15 +22,15 @@ configs=(
     # "BASE=base/segregated NAME=hex.struct.seg GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0"
     # "BASE=base/segregated NAME=tet.struct.seg GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0"
     # "BASE=base/segregated NAME=tet.unstruct.seg GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0"
-    # "BASE=base/highOrder NAME=hex.struct.ho.N1 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.ksponly HOJAC=false HORES=true"
-    # "BASE=base/highOrder NAME=hex.struct.ho.N2 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true"
-    # "BASE=base/highOrder NAME=hex.struct.ho.N3 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true"
-    "BASE=base/highOrder NAME=tet.struct.ho.N1 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true"
-    "BASE=base/highOrder NAME=tet.struct.ho.N2 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true"
-    "BASE=base/highOrder NAME=tet.struct.ho.N3 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true"
-    "BASE=base/highOrder NAME=tet.unstruct.ho.N1 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true"
-    "BASE=base/highOrder NAME=tet.unstruct.ho.N2 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true"
-    "BASE=base/highOrder NAME=tet.unstruct.ho.N3 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true"
+    # "BASE=base/highOrder NAME=hex.struct.ho.N1 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.ksponly HOJAC=false HORES=true TYPE=movingLeastSquares"
+    # "BASE=base/highOrder NAME=hex.struct.ho.N2 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=movingLeastSquares"
+    # "BASE=base/highOrder NAME=hex.struct.ho.N3 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=movingLeastSquares"
+    "BASE=base/highOrder NAME=tet.struct.ho.N1 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=movingLeastSquares"
+    "BASE=base/highOrder NAME=tet.struct.ho.N2 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=movingLeastSquares"
+    "BASE=base/highOrder NAME=tet.struct.ho.N3 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=movingLeastSquares"
+    "BASE=base/highOrder NAME=tet.unstruct.ho.N1 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=movingLeastSquares"
+    "BASE=base/highOrder NAME=tet.unstruct.ho.N2 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=movingLeastSquares"
+    "BASE=base/highOrder NAME=tet.unstruct.ho.N3 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=movingLeastSquares"
 )
 
 # Define start and end mesh indices
@@ -68,7 +68,7 @@ cd "${RUN_DIR}"
 for config in "${configs[@]}"
 do
     # Reset variables in the case some variable is not used
-    unset GMSH_FILE PETSC_FILE order extraCells HOJAC HORES
+    unset GMSH_FILE PETSC_FILE order extraCells HOJAC HORES TYPE
 
     # Parse the configuration string
     eval $config
@@ -118,6 +118,11 @@ do
             sed -i "/^\s*faceStencilExtraCells /s|^.*|        faceStencilExtraCells ${extraCells};|" constant/solidProperties
         fi
 
+        # Update the least squares type
+        if [ -n "${TYPE}" ]; then
+            sed -i "/^\s*type \(movingLeastSquares\|kExactLeastSquares\);/s|^.*|            type ${TYPE};|" constant/solidProperties
+        fi
+
         # Update how Jacobian is calculated
         if [ -n "${HOJAC}" ]; then
             sed -i "/^\s*highOrderJacobian /s|^.*|        highOrderJacobian ${HOJAC};|" constant/solidProperties

papers/JFNK_highOrder/linearElastic/cantilever/Allrun.kExact

@@ -0,0 +1,218 @@
+#!/bin/bash
+
+# Source required functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+source solids4FoamScripts.sh
+# Extend version not supported
+solids4Foam::caseDoesNotRunWithFoamExtend
+
+# solids4Foam location path
+export SOLIDS4FOAM_DIR=/Users/ivanbatistic/work/solids4foam-ib/solids4foam-ib-2412/
+echo "SOLIDS4FOAM_DIR = $SOLIDS4FOAM_DIR"
+
+# Compile the cantileverBeam library
+(cd src && ./Allwmake -j -s)
+
+# Segregated version require a lot of time to converge, I will skip it for
+# now. Tet mesh is not working with snes becouse of gradient at corner cells
+
+# Define configurations as space-separated strings
+configs=(
+    # "BASE=base/snes NAME=hex.struct.hypre-snes GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 PETSC_FILE=petscOptions.lu"
+    # "BASE=base/segregated NAME=hex.struct.seg GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0"
+    # "BASE=base/segregated NAME=tet.struct.seg GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0"
+    # "BASE=base/segregated NAME=tet.unstruct.seg GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0"
+    # "BASE=base/highOrder NAME=hex.struct.ho.N1 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.ksponly HOJAC=false HORES=true TYPE=kExactLeastSquares"
+    # "BASE=base/highOrder NAME=hex.struct.ho.N2 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=kExactLeastSquares"
+    # "BASE=base/highOrder NAME=hex.struct.ho.N3 GMSH_FILE=hex-structured USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=kExactLeastSquares"
+    "BASE=base/highOrder NAME=tet.struct.ho.N1 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=kExactLeastSquares"
+    "BASE=base/highOrder NAME=tet.struct.ho.N2 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=kExactLeastSquares"
+    "BASE=base/highOrder NAME=tet.struct.ho.N3 GMSH_FILE=tet-structured USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=kExactLeastSquares"
+    "BASE=base/highOrder NAME=tet.unstruct.ho.N1 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=1 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=kExactLeastSquares"
+    "BASE=base/highOrder NAME=tet.unstruct.ho.N2 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=2 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=kExactLeastSquares"
+    "BASE=base/highOrder NAME=tet.unstruct.ho.N3 GMSH_FILE=tet-unstructured_v2 USE_PERTURBMESHPOINTS=0 polyOrder=3 extraCells=10 PETSC_FILE=petscOptions.lu HOJAC=false HORES=true TYPE=kExactLeastSquares"
+)
+
+# Define start and end mesh indices
+# Mesh input files are defined from 1 to 15
+# END_MESH should be greater than START_MESH
+START_MESH=1
+END_MESH=15
+
+
+# Detect the CPU type: we append this to the case name
+if [[ "$OSTYPE" == "darwin"* ]]
+then
+    # macOS
+    CPU_TYPE=$(sysctl -n machdep.cpu.brand_string | sed 's/[^a-zA-Z0-9]/_/g')
+elif [[ -f /proc/cpuinfo ]]
+then
+    # Linux
+    CPU_TYPE=$(grep -m 1 "model name" /proc/cpuinfo | awk -F': ' '{print $2}' | sed 's/[^a-zA-Z0-9]/_/g')
+else
+    # Fallback if neither method works
+    CPU_TYPE="Unknown_CPU"
+fi
+
+
+# Create timestamped working directory for this run
+DATE=$(date +%Y-%m-%d_%H-%M-%S)
+RUN_DIR="run_${CPU_TYPE}_${DATE}"
+echo "Creating ${RUN_DIR}"
+mkdir "${RUN_DIR}"
+
+# Enter the run directory
+cd "${RUN_DIR}"
+
+# Iterate through configurations
+for config in "${configs[@]}"
+do
+    # Reset variables in the case some variable is not used
+    unset GMSH_FILE PETSC_FILE order extraCells HOJAC HORES TYPE
+
+    # Parse the configuration string
+    eval $config
+    echo; echo "***************************************"
+    echo "Running configuration: $config"
+    echo "***************************************"
+
+    # Define results summary file name
+    SUMMARY="${NAME}.summary.txt"
+    echo "# Mesh Time Mem CellsNumber D_L2 D_Linf S_L2 S_Linf" > "${SUMMARY}"
+
+    # Loop over mesh densities in each configuration
+    for i in `seq $START_MESH $END_MESH`
+    do
+        CASE="${NAME}.$i"
+        echo; echo "Processing case: $CASE"
+
+        # Prepare the case
+        cp -rL "../${BASE}" "${CASE}"
+        cd "$CASE"
+
+        # GMSH Mesh generation
+        cp "gmsh/meshSpacing/meshSpacing$i.geo" "gmsh/meshSpacing/meshSpacing.geo"
+        solids4Foam::runApplication gmsh -3 -format msh2 gmsh/"${GMSH_FILE}.geo"
+        solids4Foam::runApplication gmshToFoam gmsh/"${GMSH_FILE}.msh"
+        solids4Foam::runApplication changeDictionary
+
+        # Optional mesh distortion
+        if [ "$USE_PERTURBMESHPOINTS" -eq 1 ]
+        then
+            solids4Foam::runApplication perturbMeshPoints
+        fi
+        solids4Foam::runApplication checkMesh
+
+        # Update the PETSc options file
+        if [ -n "${PETSC_FILE}" ]; then
+            sed -i "/^\s*optionsFile /s|^.*|    optionsFile ${PETSC_FILE};|" constant/solidProperties
+        fi
+
+        # Update the order
+        if [ -n "${polyOrder}" ]; then
+            sed -i "/^\s*polynomialOrder /s|^.*|        polynomialOrder ${polyOrder};|" constant/solidProperties
+        fi
+
+        # Update number of stencil cells
+        if [ -n "${extraCells}" ]; then
+            sed -i "/^\s*faceStencilExtraCells /s|^.*|        faceStencilExtraCells ${extraCells};|" constant/solidProperties
+        fi
+
+        # Update the least squares type
+        if [ -n "${TYPE}" ]; then
+            sed -i "/^\s*type \(movingLeastSquares\|kExactLeastSquares\);/s|^.*|            type ${TYPE};|" constant/solidProperties
+        fi
+
+        # Update how Jacobian is calculated
+        if [ -n "${HOJAC}" ]; then
+            sed -i "/^\s*highOrderJacobian /s|^.*|        highOrderJacobian ${HOJAC};|" constant/solidProperties
+        fi
+
+        # Update how Residual is calculated
+        if [ -n "${HORES}" ]; then
+            sed -i "/^\s*highOrderResidual /s|^.*|        highOrderResidual ${HORES};|" constant/solidProperties
+        fi
+
+        # Run the solver
+        # If "gtime" is available (could be called "time" on Linux), use it to
+        # record the max memory usage
+        if command -v gtime &> /dev/null
+        then
+            echo "Running solids4Foam on ${CASE} with gtime"
+            gtime -f "gtime/time (wall clock) time: %e\nMaximum resident set size (kbytes): %M" solids4Foam &> log.solids4Foam
+
+        elif [ -x /usr/bin/time ]
+        then
+            echo "Running solids4Foam on ${CASE} with /usr/bin/time"
+            /usr/bin/time -f "gtime/time (wall clock) time: %e\nMaximum resident set size (kbytes): %M" solids4Foam &> log.solids4Foam
+
+        elif command -v time &> /dev/null
+        then
+            echo "Running solids4Foam on ${CASE} with shell builtin time (no max memory)"
+            time solids4Foam &> log.solids4Foam
+
+        else
+            echo "Running solids4Foam on ${CASE}"
+            solids4Foam::runApplication solids4Foam
+        fi
+
+        # Extract results from solver log and append them to a summary file
+        echo; echo "Appending results to ${SUMMARY}"
+        if grep -q "gtime/time" log.solids4Foam; then
+            CLOCK_TIME=$(grep "gtime/time" log.solids4Foam | awk '{print $5}')
+        else
+            # Record the time
+            CLOCK_TIME=$(grep "ClockTime" log.solids4Foam | awk '{print $7}')
+        fi
+
+        # Extract results from solver log and append them to a summary file
+        if grep -q "Maximum resident" log.solids4Foam; then
+            MAX_MEMORY=$(grep "Maximum resident" log.solids4Foam | awk '{print int($6 / 1000)}')
+        else
+            MAX_MEMORY="NaN"
+        fi
+
+        # Number of cells
+        CELLS=$(grep "cells:" log.checkMesh | awk '{print $2}')
+
+        # Extract the L2 (average) error for displacement
+        DISP_L2_ERROR=$(grep "Writing DDifference field" -A 2 log.solids4Foam | tail -1 | awk '{print $3}')
+
+        # Extract the LInfinity (max) error for displacement
+        DISP_LINF_ERROR=$(grep "Writing DDifference field" -A 2 log.solids4Foam | tail -1 | awk '{print $4}')
+
+        # Extract the L2 (average) error for mag(sigma)
+        STRESS_L2_ERROR=$(grep "Writing sigmaDifference field" -A 2 log.solids4Foam | tail -1 | awk '{print $3}')
+
+        # Extract the LInfinity (max) error for mag(sigma)
+        STRESS_LINF_ERROR=$(grep "Writing sigmaDifference field" -A 2 log.solids4Foam | tail -1 | awk '{print $4}')
+
+        # Write data to file
+        echo "$i $CLOCK_TIME $MAX_MEMORY $CELLS $DISP_L2_ERROR $DISP_LINF_ERROR $STRESS_L2_ERROR $STRESS_LINF_ERROR" >> ../"${SUMMARY}"
+
+        cd ..
+    done
+
+    # Print summary file
+    echo; echo "${SUMMARY} file:"; cat "${SUMMARY}"; echo
+
+done
+
+# Create plots if gnuplot in installed
+if command -v gnuplot &>/dev/null
+then
+    # Copy gnuplot scripts
+    cp ../plotScripts/*gnuplot .
+
+    # Run all scripts
+    for f in *gnuplot
+    do
+        echo "Running gnuplot on $f"
+        gnuplot "$f" 2>/dev/null
+    done
+fi
+
+echo; echo; echo "Done!"; echo
+echo "View the PDF files in ${RUN_DIR}"
+echo; echo $(date)
+echo; echo

papers/JFNK_highOrder/linearElastic/cantilever/base/highOrder/constant/solidProperties

@@ -33,6 +33,7 @@ linearGeometryTotalDisplacementCoeffs
 
         displacement
         {
+            type movingLeastSquares;
             polynomialOrder 2;
             faceStencilExtraCells 10;