Merge pull request #2360 from KratosMultiphysics/feature-poro-analysis

Updating Poromechanics analysis and solver to new standard
KratosMultiphysics · Jun 23, 2018 · c4c4fc3 · c4c4fc3
2 parents 36c9fa2 + 4420597
commit c4c4fc3
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diff --git a/applications/PoromechanicsApplication/README.md b/applications/PoromechanicsApplication/README.md
@@ -4,17 +4,17 @@ The Poromechanics Application contains developments in coupled solid-pore fluid
 
 ### Features:
 
-- UPw small displacement element for saturated porous media (with 
+- UPw small displacement element for saturated porous media (with
 equal order interpolation, unstable under incompressible-undrained
 conditions)
 
-- Stable UPw small displacement element for saturated porous media 
+- Stable UPw small displacement element for saturated porous media
 (with higher order interpolation for displacements)
 
-- FIC-Stabilized UPw small displacement element for saturated porous media 
+- FIC-Stabilized UPw small displacement element for saturated porous media
 (with equal order interpolation for displacements)
 
-- UPw Quasi-zero-thickness interface elements for defining cracks and 
+- UPw Quasi-zero-thickness interface elements for defining cracks and
 joints
 
 - Local linear elastic damage model (Simo-Ju and modified Von Mises)
@@ -24,8 +24,8 @@ Mises)
 
 - Bilinear cohesive fracture model (for quasi-zero-thickness interface elements)
 
-- Fracture propagation utility based on the combination of the 
-damage model with the insertion of interface elements after remeshing 
+- Fracture propagation utility based on the combination of the
+damage model with the insertion of interface elements after remeshing
 with GiD
 
 
@@ -61,8 +61,8 @@ Make sure that the following lines are properly set in the configure.sh file:
 >
 > -DUSE_PORO_MPI=ON \\
 
-Uncomment the following line in 
-[poromechanics_main.py](https://github.com/KratosMultiphysics/Kratos/blob/master/applications/PoromechanicsApplication/custom_problemtype/Poromechanics_Application.gid/poromechanics_main.py) and [poromechanics_fracture_main.py](https://github.com/KratosMultiphysics/Kratos/blob/master/applications/PoromechanicsApplication/custom_problemtype/Poromechanics_Application.gid/poromechanics_fracture_main.py).
+Uncomment the following line in
+[KratosPoromechanics.py](https://github.com/KratosMultiphysics/Kratos/blob/master/applications/PoromechanicsApplication/custom_problemtype/Poromechanics_Application.gid/KratosPoromechanics.py).
 
 > import KratosMultiphysics.TrilinosApplication as TrilinosApplication
 

diff --git a/...hanicsApplication/custom_problemtype/Poromechanics_Application.gid/KratosPoromechanics.py b/...hanicsApplication/custom_problemtype/Poromechanics_Application.gid/KratosPoromechanics.py
@@ -0,0 +1,19 @@
+from __future__ import print_function, absolute_import, division #makes KratosMultiphysics backward compatible with python 2.6 and 2.7
+
+import KratosMultiphysics
+import KratosMultiphysics.ExternalSolversApplication
+# import KratosMultiphysics.TrilinosApplication as TrilinosApplication
+import KratosMultiphysics.FluidDynamicsApplication
+import KratosMultiphysics.SolidMechanicsApplication
+import KratosMultiphysics.PoromechanicsApplication
+
+from poromechanics_analysis import PoromechanicsAnalysis
+
+if __name__ == "__main__":
+
+    with open("ProjectParameters.json",'r') as parameter_file:
+        parameters = KratosMultiphysics.Parameters(parameter_file.read())
+
+    model = KratosMultiphysics.Model()
+    simulation = PoromechanicsAnalysis(model,parameters)
+    simulation.Run()
diff --git a/...pplication/custom_problemtype/Poromechanics_Application.gid/Poromechanics_Application.prb b/...pplication/custom_problemtype/Poromechanics_Application.gid/Poromechanics_Application.prb
@@ -34,7 +34,7 @@ VALUE: 0.05
 HELP: Length defining the domain of interaction between non-local damaged points.
 QUESTION: Fracture_Propagation#CB#(true,false)
 VALUE: false
-HELP: Only for pre-defined crack-tips defined with interface elements.
+HELP: Only for pre-defined crack tips defined with interface elements.
 DEPENDENCIES: (true,RESTORE,Propagation_Length,#CURRENT#,RESTORE,Propagation_Damage,#CURRENT#,RESTORE,Propagation_Frequency,#CURRENT#,RESTORE,Propagation_Width,#CURRENT#,RESTORE,Propagation_Height,#CURRENT#,RESTORE,Correction_Tolerance,#CURRENT#)(false,HIDE,Propagation_Length,#CURRENT#,HIDE,Propagation_Damage,#CURRENT#,HIDE,Propagation_Frequency,#CURRENT#,HIDE,Propagation_Width,#CURRENT#,HIDE,Propagation_Height,#CURRENT#,HIDE,Correction_Tolerance,#CURRENT#)
 QUESTION: Propagation_Damage
 VALUE: 0.5
@@ -57,8 +57,8 @@ HELP: Number of steps after which the fracture propagation will be checked. Set
 
 
 TITLE:Solver_Settings
-QUESTION: Solution_Type#CB#(Quasi-Static,Dynamic)
-VALUE: Quasi-Static
+QUESTION: Solution_Type#CB#(quasi_static,Dynamic)
+VALUE: quasi_static
 QUESTION: Scheme_Type#CB#(Newmark)
 VALUE: Newmark
 QUESTION: Newmark_Beta
@@ -72,9 +72,9 @@ QUESTION: Rayleigh_Mass
 VALUE: 0.0
 QUESTION: Rayleigh_Stiffness
 VALUE: 0.0
-QUESTION: Strategy_Type#CB#(Newton-Raphson,Arc-Length)
-VALUE: Newton-Raphson
-DEPENDENCIES: (Newton-Raphson,HIDE,Desired_Iterations,#CURRENT#,HIDE,Max_Radius_Factor,#CURRENT#,HIDE,Min_Radius_Factor,#CURRENT#)(Arc-Length,RESTORE,Desired_Iterations,#CURRENT#,RESTORE,Max_Radius_Factor,#CURRENT#,RESTORE,Min_Radius_Factor,#CURRENT#)
+QUESTION: Strategy_Type#CB#(newton_raphson,arc_length)
+VALUE: newton_raphson
+DEPENDENCIES: (newton_raphson,HIDE,Desired_Iterations,#CURRENT#,HIDE,Max_Radius_Factor,#CURRENT#,HIDE,Min_Radius_Factor,#CURRENT#)(arc_length,RESTORE,Desired_Iterations,#CURRENT#,RESTORE,Max_Radius_Factor,#CURRENT#,RESTORE,Min_Radius_Factor,#CURRENT#)
 QUESTION: Convergence_Criterion#CB#(Displacement_criterion,Residual_criterion,And_criterion,Or_criterion)
 VALUE: Displacement_criterion
 DEPENDENCIES: (Displacement_criterion,RESTORE,Displacement_Relative_Tolerance,#CURRENT#,RESTORE,Displacement_Absolute_Tolerance,#CURRENT#,HIDE,Residual_Relative_Tolerance,#CURRENT#,HIDE,Residual_Absolute_Tolerance,#CURRENT#)(Residual_criterion,HIDE,Displacement_Relative_Tolerance,#CURRENT#,HIDE,Displacement_Absolute_Tolerance,#CURRENT#,RESTORE,Residual_Relative_Tolerance,#CURRENT#,RESTORE,Residual_Absolute_Tolerance,#CURRENT#)(And_criterion,RESTORE,Displacement_Relative_Tolerance,#CURRENT#,RESTORE,Displacement_Absolute_Tolerance,#CURRENT#,RESTORE,Residual_Relative_Tolerance,#CURRENT#,RESTORE,Residual_Absolute_Tolerance,#CURRENT#)(Or_criterion,RESTORE,Displacement_Relative_Tolerance,#CURRENT#,RESTORE,Displacement_Absolute_Tolerance,#CURRENT#,RESTORE,Residual_Relative_Tolerance,#CURRENT#,RESTORE,Residual_Absolute_Tolerance,#CURRENT#)

diff --git a/...pplication/custom_problemtype/Poromechanics_Application.gid/Poromechanics_Application.tcl b/...pplication/custom_problemtype/Poromechanics_Application.gid/Poromechanics_Application.tcl
@@ -1,30 +1,30 @@
 ## GiD events --------------------------------------------------------------------------------------------------------------------------------------------------
 
 proc InitGIDProject { dir } {
-    
+
     # Initialize ProblemType Menu
-    if { [GidUtils::IsTkDisabled] eq 0} {  
+    if { [GidUtils::IsTkDisabled] eq 0} {
         GiDMenu::Create "Poromechanics Application" PRE
         GiDMenu::InsertOption "Poromechanics Application" [list "Parts"] 0 PRE "GidOpenConditions \"Parts\"" "" ""
         GiDMenu::InsertOption "Poromechanics Application" [list "Dirichlet Constraints"] 1 PRE "GidOpenConditions \"Dirichlet_Constraints\"" "" ""
         GiDMenu::InsertOption "Poromechanics Application" [list "Loads"] 2 PRE "GidOpenConditions \"Loads\"" "" ""
         GiDMenu::InsertOption "Poromechanics Application" [list "Project Parameters"] 3 PRE "GidOpenProblemData" "" ""
         GiDMenu::UpdateMenus
     }
-    
+
     # Save ProblemTypePath
     set ::Poromechanics_Application::ProblemTypePath $dir
 }
 
 #-------------------------------------------------------------------------------
 
 proc AfterReadGIDProject { filename } {
-    
+
     # Save ProblemPath
     set projectpath $filename
     append projectpath .gid
     set ::Poromechanics_Application::ProblemPath $projectpath
-    
+
     # Save ProblemName
     # if {$::tcl_platform(platform) eq "windows"} {}
     if {[regexp -all {\\} $filename] > 0} {
@@ -41,10 +41,10 @@ proc AfterReadGIDProject { filename } {
 #-------------------------------------------------------------------------------
 
 proc BeforeRunCalculation { batfilename basename dir problemtypedir gidexe args } {
-    
+
     # Set Parallel Configuration
     set paralleltype [GiD_AccessValue get gendata Parallel_Configuration]
-    
+
     # Write Initial fractures data
     if {([GiD_AccessValue get gendata Fracture_Propagation] eq true) && ($paralleltype ne "MPI")} {
         # Define GiDPath
@@ -53,14 +53,14 @@ proc BeforeRunCalculation { batfilename basename dir problemtypedir gidexe args
             regsub -all {\\} $gidexe {/} gidexe
         }
         set gidexe [string trimright $gidexe gid.exe]
-        
+
         if {[GiD_AccessValue get gendata Domain_Size] eq 2} {
-        
+
             source [file join $problemtypedir FracturePropagation2D.tcl]
             WriteInitialFracturesData $dir $problemtypedir $gidexe
-        
+
         } else {
-            
+
             source [file join $problemtypedir FracturePropagation3D.tcl]
             WriteInitialFracturesData $dir $problemtypedir $gidexe
         }
@@ -73,14 +73,14 @@ proc BeforeRunCalculation { batfilename basename dir problemtypedir gidexe args
     # Write ProjectParameters
     source [file join $problemtypedir ProjectParameters.tcl]
     WriteProjectParameters $basename $dir $problemtypedir $TableDict
-    
+
     # Copy python script in the problemdir
     if {[GiD_AccessValue get gendata Fracture_Propagation] eq true} {
         file copy -force [file join $problemtypedir poromechanics_fracture_main.py] [file join $dir MainKratos.py]
     } else {
-        file copy -force [file join $problemtypedir poromechanics_main.py] [file join $dir MainKratos.py]
+        file copy -force [file join $problemtypedir KratosPoromechanics.py] [file join $dir MainKratos.py]
     }
-    
+
     # Run the problem
     set run 1
     catch {
@@ -93,7 +93,7 @@ proc BeforeRunCalculation { batfilename basename dir problemtypedir gidexe args
                                     Input files have been written.\n\
                                     Run the case with: mpirun -np \[npartitions\] python3 MainKratos.py" ]]
     }
-    
+
     ### Measure time
     #set start_time_1 [clock clicks]
     #set end_time_1 [expr { [clock clicks]-$start_time_1 }]
@@ -128,7 +128,7 @@ proc Poromechanics_Application::PropagateFractures2D { } {
     # Write new ProjectParameters
     source [file join $::Poromechanics_Application::ProblemTypePath ProjectParameters.tcl]
     WriteProjectParameters $::Poromechanics_Application::ProblemName $::Poromechanics_Application::ProblemPath $::Poromechanics_Application::ProblemTypePath $TableDict
-        
+
     # Quit GiD
     GiD_Process Mescape Files Save
     GiD_Process escape escape escape escape escape Quit
@@ -137,7 +137,7 @@ proc Poromechanics_Application::PropagateFractures2D { } {
 #-------------------------------------------------------------------------------
 
 proc Poromechanics_Application::PropagateFractures3D { } {
-    
+
     # Source Propagation Data and file
     set PropagationData [source [file join $::Poromechanics_Application::ProblemPath PropagationData.tcl]]
     source [file join $::Poromechanics_Application::ProblemTypePath FracturePropagation3D.tcl]
@@ -152,7 +152,7 @@ proc Poromechanics_Application::PropagateFractures3D { } {
     # Write new ProjectParameters
     source [file join $::Poromechanics_Application::ProblemTypePath ProjectParameters.tcl]
     WriteProjectParameters $::Poromechanics_Application::ProblemName $::Poromechanics_Application::ProblemPath $::Poromechanics_Application::ProblemTypePath $TableDict
-    
+
     # Quit GiD
     GiD_Process Mescape Files Save
     GiD_Process escape escape escape escape escape Quit
@@ -161,60 +161,60 @@ proc Poromechanics_Application::PropagateFractures3D { } {
 #--------------------------------------------------------------------------------------------------------------------------------------------------------------
 
 proc Poromechanics_Application::CreateContactEntity { } {
-    
+
     set LayerName "Layer0"
-    
+
     ## Contact Surface:
-    
+
     # set Line1 [list 111 1]
     # set Line2 [list 110 0]
-    
+
     # # Orientation of Line1:
     # #     0: SAME1ST. The normal to the line points towards the oppsite direction of the contact surface.
     # #     1: DIFF1ST. The normal to the line points towards the contact surface.
     # # Orientation of Line2:
     # #     0: SAME1ST. The normal to the line points towards the contact surface.
     # #     1: DIFF1ST. The normal to the line points towards the oppsite direction of the contact surface.
-    
+
     # GiD_Geometry create surface append contactsurface \
     #     $LayerName 2 $Line1 $Line2
-    
-    
+
+
     ## Contact Volume:
 
     # set Surf1 [list 5 1]
     # set Surf2 [list 186 0]
-        
+
     # # Orientation of Surf1:
     # #     0: SAME1ST. The normal to the surface points towards the contact volume.
     # #     1: DIFF1ST. The normal to the surface points towards the oppsite direction of the contact volume.
     # # Orientation of Surf2:
     # #     0: DIFF1ST. The normal to the surface points towards the oppsite direction of the contact volume.
     # #     1: SAME1ST. The normal to the surface points towards the contact volume.
-    
+
     # Transformation matrix for a contact volume between Surf1 and Surf2. R means rotation, and T translation.
-    
+
     # set TransformMatrix [list Rxx Rxy Rxz Tx \
     #                           Ryx Ryy Ryz Ty \
     #                           Rzx Rzy Rzz Tz \
     #                           0.0 0.0 0.0 1.0]
-    
+
     # Transformation matrix for a contact volume between two equal surfaces, one over the other (zero-thickness interface elements)
-    
+
     # set TransformMatrix [list 1.0 0.0 0.0 0.0 \
     #                           0.0 1.0 0.0 0.0 \
     #                           0.0 0.0 1.0 0.0 \
     #                           0.0 0.0 0.0 1.0]
-    
+
     # Transformation matrix for a contact volume generated by a translation from Surf1 to Surf2
-    
+
     # set TransformMatrix [list 1.0 0.0 0.0 Tx \
     #                           0.0 1.0 0.0 Ty \
     #                           0.0 0.0 1.0 Tz \
     #                           0.0 0.0 0.0 1.0]
 
     # Transformation matrix for a contact volume generated by a normal translation from Surf1 to Surf2
-    
+
     # # Vertex of Surf1
     # set Vertex [GiD_Geometry get point 90]
     # # Point1 of Surf1
@@ -226,7 +226,7 @@ proc Poromechanics_Application::CreateContactEntity { } {
     # set TransformMatrix [NormalTranslationMatrix $Vertex $Point1 $Point2 $Distance]
 
     # Transformation matrix for a contact volume generated by a rotation around a given axis from Surf1 to Surf2:
-    
+
     # # Point at the initial position of the rotation
     # set InitPoint [GiD_Geometry get point 17]
     # # Point at the final position of the rotation
@@ -238,7 +238,7 @@ proc Poromechanics_Application::CreateContactEntity { } {
     # # Final point of the rotation Axis
     # set FinalAxis [GiD_Geometry get point 19]
     # set TransformMatrix [RotationMatrix $InitPoint $FinalPoint $Vertex $InitAxis $FinalAxis]
-        
+
     # GiD_Geometry create volume append $LayerName 2 \
     #    $Surf1 $Surf2 contactvolume $TransformMatrix
 }
@@ -255,20 +255,20 @@ proc NormalTranslationMatrix {Vertex Point1 Point2 Distance} {
     set Vy(0) [expr {[lindex $Point2 1]-[lindex $Vertex 1]}]
     set Vy(1) [expr {[lindex $Point2 2]-[lindex $Vertex 2]}]
     set Vy(2) [expr {[lindex $Point2 3]-[lindex $Vertex 3]}]
-    
-    # Vector in local z direction (Cross product between Vx and Vy)    
+
+    # Vector in local z direction (Cross product between Vx and Vy)
     set Vz(0) [expr {$Vx(1)*$Vy(2)-$Vx(2)*$Vy(1)}]
     set Vz(1) [expr {$Vx(2)*$Vy(0)-$Vx(0)*$Vy(2)}]
     set Vz(2) [expr {$Vx(0)*$Vy(1)-$Vx(1)*$Vy(0)}]
     set InvNorm [expr {1.0/sqrt($Vz(0)*$Vz(0)+$Vz(1)*$Vz(1)+$Vz(2)*$Vz(2))}]
     set Vz(0) [expr {$Vz(0)*$InvNorm}]
     set Vz(1) [expr {$Vz(1)*$InvNorm}]
     set Vz(2) [expr {$Vz(2)*$InvNorm}]
-    
+
     set Tx [expr {$Distance*Vz(0)}]
     set Ty [expr {$Distance*Vz(1)}]
     set Tz [expr {$Distance*Vz(2)}]
-    
+
     return [list 1.0 0.0 0.0 $Tx \
                  0.0 1.0 0.0 $Ty \
                  0.0 0.0 1.0 $Tz \
@@ -303,7 +303,7 @@ proc RotationMatrix {InitPoint FinalPoint Vertex InitAxis FinalAxis} {
     set A(0) [expr {$A(0)*$InvNorm}]
     set A(1) [expr {$A(1)*$InvNorm}]
     set A(2) [expr {$A(2)*$InvNorm}]
-    
+
     # Cosine of the angle of rotation
     set CosAngle [expr {$Ri(0)*$Rf(0)+$Ri(1)*$Rf(1)+$Ri(2)*$Rf(2)}]
     # Cross product between vectors Ri and Rf
@@ -312,7 +312,7 @@ proc RotationMatrix {InitPoint FinalPoint Vertex InitAxis FinalAxis} {
     set n(2) [expr {$Ri(0)*$Rf(1)-$Ri(1)*$Rf(0)}]
     # Sine of the angle of rotation (positive angle between 0º and 90º)
     set SinAngle [expr {sqrt($n(0)*$n(0)+$n(1)*$n(1)+$n(2)*$n(2))}]
-    
+
     # Transformation Matrix
     set Rxx [expr {$CosAngle+$A(0)*$A(0)*(1.0-$CosAngle)}]
     set Rxy [expr {$A(0)*$A(1)*(1.0-$CosAngle)-$A(2)*$SinAngle}]
@@ -326,7 +326,7 @@ proc RotationMatrix {InitPoint FinalPoint Vertex InitAxis FinalAxis} {
     set Tx [expr {[lindex $InitAxis 1]-($Rxx*[lindex $InitAxis 1]+$Rxy*[lindex $InitAxis 2]+$Rxz*[lindex $InitAxis 3])}]
     set Ty [expr {[lindex $InitAxis 2]-($Ryx*[lindex $InitAxis 1]+$Ryy*[lindex $InitAxis 2]+$Ryz*[lindex $InitAxis 3])}]
     set Tz [expr {[lindex $InitAxis 3]-($Rzx*[lindex $InitAxis 1]+$Rzy*[lindex $InitAxis 2]+$Rzz*[lindex $InitAxis 3])}]
-    
+
     return [list $Rxx $Rxy $Rxz $Tx \
                  $Ryx $Ryy $Ryz $Ty \
                  $Rzx $Rzy $Rzz $Tz \

diff --git a/...ation/custom_problemtype/Poromechanics_Application.gid/Poromechanics_Application.unix.bat b/...ation/custom_problemtype/Poromechanics_Application.gid/Poromechanics_Application.unix.bat
@@ -16,15 +16,15 @@ export PYTHONPATH="$HOME/Kratos:$PYTHONPATH"
 
 ## Linux
 # Setting PATHs for Kratos libs
-export LD_LIBRARY_PATH="$HOME/Kratos/libs:$HOME/boost_1_62_0/stage/lib:$LD_LIBRARY_PATH"
+export LD_LIBRARY_PATH="$HOME/Kratos/libs:$LD_LIBRARY_PATH"
 # Setting PATH for Python 3
 export PATH="/usr/bin/python3:$PATH"
 
 ## OS X
-#~ # Setting PATHs for Kratos
-#~ export DYLD_LIBRARY_PATH="$HOME/Kratos/libs:$HOME/boost_1_62_0/stage/lib:$DYLD_LIBRARY_PATH"
-#~ # Setting PATH for Python 3
-#~ export PATH="/Library/Frameworks/Python.framework/Versions/3.5/bin:${PATH}"
+# # Setting PATHs for Kratos
+# export DYLD_LIBRARY_PATH="$HOME/Kratos/libs:$DYLD_LIBRARY_PATH"
+# # Setting PATH for Python 3
+# export PATH="/Library/Frameworks/Python.framework/Versions/3.6/bin:${PATH}"
 
 # Execute the program
 "python3" "MainKratos.py" > "$1.info" 2> "$1.err"