Fluid write with geometries

.gitignore

@@ -15,3 +15,4 @@ dist
 *.tgz
 null
 __pycache__
+*.whl

dockers/dockerfile

@@ -1,5 +1,5 @@
 # Default values. Use --build-arg on build to change
-ARG pyversion=3.10.8
+ARG pyversion=3.11
 
 # Base pyton image
 FROM python:$pyversion
@@ -8,10 +8,14 @@ FROM python:$pyversion
 # Update pip
 RUN pip install --upgrade pip
 
-ARG krversion=9.3.2
+ARG krversion=9.4.2
+
+# WORKDIR /tmp
+# COPY ./wheels/ ./wheels/
 
 # Install Kratos and dependencies
 RUN python3 -m pip install KratosMultiphysics-all==$krversion numpy
+# RUN python3 -m pip install ./wheels/*.whl
 
 # Prepare run folder
 WORKDIR "/model"

kratos.gid/apps/Buoyancy/app.json

@@ -37,7 +37,8 @@
     "write": {
         "coordinates": "all",
         "properties_location": "json",
-        "model_part_name": "ThermalModelPart"
+        "model_part_name": "ThermalModelPart",
+        "write_mdpa_mode": "entities"
     },
     "main_launch_file": "../../exec/MainKratos.py",
     "examples": "examples/examples.xml"

kratos.gid/apps/Buoyancy/write/write.tcl

@@ -20,6 +20,8 @@ proc ::Buoyancy::write::writeModelPartEvent { } {
 
     # Start Fluid write variables
     Fluid::write::Init
+    # Fluid has implemented the geometry mode, but we do not use it yet in inherited apps
+    ::Fluid::write::SetAttribute write_mdpa_mode [::Buoyancy::GetWriteProperty write_mdpa_mode]
     # Start Fluid write conditions map from scratch
     Fluid::write::InitConditionsMap
 

kratos.gid/apps/CompressibleFluid/app.json

@@ -42,7 +42,8 @@
         "materials_file": "FluidMaterials.json",
         "properties_location": "json",
         "model_part_name": "FluidModelPart",
-        "output_model_part_name": "fluid_computational_model_part"
+        "output_model_part_name": "fluid_computational_model_part",
+        "write_mdpa_mode": "entities"
     },
     "main_launch_file": "python/MainKratos.py",
     "examples": "examples/examples.xml",

kratos.gid/apps/CompressibleFluid/write/write.tcl

@@ -10,6 +10,8 @@ namespace eval ::CompressibleFluid::write {
 proc ::CompressibleFluid::write::Init { } {
     # Namespace variables inicialization
     ::Fluid::write::Init
+    # Fluid has implemented the geometry mode, but we do not use it yet in inherited apps
+    ::Fluid::write::SetAttribute write_mdpa_mode [::CompressibleFluid::GetWriteProperty write_mdpa_mode]
 
     SetAttribute parts_un            [::Fluid::GetUniqueName parts]
     SetAttribute nodal_conditions_un [::CompressibleFluid::GetUniqueName nodal_conditions]

kratos.gid/apps/EmbeddedFluid/app.json

@@ -40,7 +40,8 @@
     "write": {
         "coordinates": "all",
         "materials_file": "FluidMaterials.json",
-        "properties_location": "json"
+        "properties_location": "json",
+        "write_mdpa_mode": "entities"
     },
     "main_launch_file": "../../exec/MainKratos.py",
     "examples": "examples/examples.xml"

kratos.gid/apps/EmbeddedFluid/write/write.tcl

@@ -8,6 +8,8 @@ namespace eval ::EmbeddedFluid::write {
 proc EmbeddedFluid::write::Init { } {
     # Namespace variables inicialization        
     variable writeAttributes
+    # Fluid has implemented the geometry mode, but we do not use it yet in inherited apps
+    ::Fluid::write::SetAttribute write_mdpa_mode [::EmbeddedFluid::GetWriteProperty write_mdpa_mode]
     set writeAttributes [::Fluid::write::GetAttributes]
 }
 

kratos.gid/apps/FSI/app.json

@@ -53,7 +53,8 @@
         "materials_file": "StructuralMaterials.json",
         "properties_location": "json",
         "model_part_name": "Structure",
-        "enable_dynamic_substepping": false
+        "enable_dynamic_substepping": false,
+        "write_mdpa_mode": "entities"
     },
     "main_launch_file": "../../exec/MainKratos.py",
     "examples": "examples/examples.xml"

kratos.gid/apps/FSI/write/write.tcl

@@ -23,6 +23,8 @@ proc ::FSI::write::writeModelPartEvent { } {
     set filename [Kratos::GetModelName]
 
     Fluid::write::Init
+    # Fluid has implemented the geometry mode, but we do not use it yet in inherited apps
+    ::Fluid::write::SetAttribute write_mdpa_mode [::FSI::GetWriteProperty write_mdpa_mode]
     Fluid::write::InitConditionsMap
     Fluid::write::SetCoordinatesByGroups 1
     write::writeAppMDPA Fluid

kratos.gid/apps/Fluid/app.json

@@ -45,7 +45,8 @@
         "materials_file": "FluidMaterials.json",
         "properties_location": "json",
         "model_part_name": "FluidModelPart",
-        "output_model_part_name": "fluid_computational_model_part"
+        "output_model_part_name": "fluid_computational_model_part",
+        "write_mdpa_mode": "geometries"
     },
     "main_launch_file": "../../exec/MainKratos.py",
     "examples": "examples/examples.xml",

kratos.gid/apps/Fluid/write/write.tcl

@@ -1,7 +1,7 @@
 namespace eval ::Fluid::write {
     namespace path ::Fluid
     Kratos::AddNamespace [namespace current]
-
+    
     # Namespace variables declaration
     variable writeCoordinatesByGroups
     variable writeAttributes
@@ -20,15 +20,24 @@ proc ::Fluid::write::Init { } {
     SetAttribute results_un [::Fluid::GetUniqueName results]
     SetAttribute drag_un [::Fluid::GetUniqueName drag]
     SetAttribute time_parameters_un [::Fluid::GetUniqueName time_parameters]
-
+    
     SetAttribute writeCoordinatesByGroups [::Fluid::GetWriteProperty coordinates]
     SetAttribute validApps [list "Fluid"]
     SetAttribute main_launch_file [::Fluid::GetAttribute main_launch_file]
     SetAttribute materials_file [::Fluid::GetWriteProperty materials_file]
     SetAttribute properties_location [::Fluid::GetWriteProperty properties_location]
     SetAttribute model_part_name [::Fluid::GetWriteProperty model_part_name]
     SetAttribute output_model_part_name [::Fluid::GetWriteProperty output_model_part_name]
-
+    SetAttribute write_mdpa_mode [::Fluid::GetWriteProperty write_mdpa_mode]
+    # Only write as geometries if the app says it AND the user allows it
+    # Note: Fluid will enable it but most of the apps that derive from Fluid are not ready for it
+    # Also user can disable it by setting the variable experimental_write_geometries to 0 in the preferences window
+    set write_geometries_enabled 0
+    if {[info exists Kratos::kratos_private(experimental_write_geometries)] && $Kratos::kratos_private(experimental_write_geometries)>0} {set write_geometries_enabled 1}
+    if {[GetAttribute write_mdpa_mode] eq "geometries" && $write_geometries_enabled ne 1} {
+        SetAttribute write_mdpa_mode "entities"
+    }
+
     variable last_condition_iterator
     set last_condition_iterator 0
 }
@@ -38,35 +47,71 @@ proc ::Fluid::write::writeModelPartEvent { } {
     # Validation
     set err [Validate]
     if {$err ne ""} {error $err}
-
+    
     InitConditionsMap
-
+    
     # Init data
     write::initWriteConfiguration [GetAttributes]
-
+    
     # Headers
     write::writeModelPartData
     writeProperties
-
+    
     # Nodal coordinates (1: Print only Fluid nodes <inefficient> | 0: the whole mesh <efficient>)
     if {[GetAttribute writeCoordinatesByGroups] ne "all"} {write::writeNodalCoordinatesOnParts} {write::writeNodalCoordinates}
 
-    # Element connectivities (Groups on FLParts)
-    write::writeElementConnectivities
-
-    # Nodal conditions and conditions
-    writeConditions
-
-    # Custom SubmodelParts
-    variable last_condition_iterator
-    write::writeBasicSubmodelPartsByUniqueId $Fluid::write::FluidConditionMap $last_condition_iterator
-
-    # SubmodelParts
-    writeMeshes
+    if {[GetAttribute write_mdpa_mode] eq "geometries"} {
+        # Write geometries
+        # Get the list of groups in the spd
+        set lista [::Fluid::xml::GetListOfSubModelParts]
+
+        # Write the geometries
+        set ret [::write::writeGeometryConnectivities $lista]
+
+        # Write the submodelparts
+        set grouped_conditions [dict create]
+        foreach group $lista {
+            # Some conditions should be grouped in the same submodelpart
+            # Get condition 
+            set condition_node [$group parent]
+            # W "Condition node: $condition_node"
+            set condition_name [$condition_node @n]
+            # W "Condition name: $condition_name"
+            set condition [Model::getCondition $condition_name]
+            if {$condition ne "" && [$condition getGroupBy] eq "Condition"} {
+                dict lappend grouped_conditions $condition [$group @n]
+            } else {
+                write::writeGroupSubModelPartAsGeometry [$group @n]
+            }
+        }
 
-    # Write custom blocks at the end of the file
-    writeCustomBlocks
+        # Write the grouped conditions
+        foreach condition [dict keys $grouped_conditions] {
+            set condition_name [$condition getName]
+            set new_group_name "_HIDDEN_$condition_name"
+            set groups [dict get $grouped_conditions $condition]
+            set new_group [spdAux::MergeGroups $new_group_name $groups]
+            write::writeGroupSubModelPartAsGeometry $new_group_name 
+            GiD_Groups delete $new_group_name
+        }
 
+    } else {
+        # Element connectivities (Groups on FLParts)
+        write::writeElementConnectivities
+
+        # Nodal conditions and conditions
+        writeConditions
+
+        # Custom SubmodelParts
+        variable last_condition_iterator
+        write::writeBasicSubmodelPartsByUniqueId $Fluid::write::FluidConditionMap $last_condition_iterator
+        # SubmodelParts
+        writeMeshes
+
+        # Write custom blocks at the end of the file
+        writeCustomBlocks
+    }
+
     # Clean
     unset ::Fluid::write::FluidConditionMap
 }
@@ -79,30 +124,43 @@ proc ::Fluid::write::writeCustomFilesEvent { } {
 
 # Custom files
 proc ::Fluid::write::WriteMaterialsFile { {write_const_law True} {include_modelpart_name True} } {
+
     set model_part_name ""
     if {[write::isBooleanTrue $include_modelpart_name]} {set model_part_name [GetAttribute model_part_name]}
-    write::writePropertiesJsonFile [GetAttribute parts_un] [GetAttribute materials_file] $write_const_law $model_part_name
+    write::writePropertiesJsonFileDone [GetAttribute materials_file] [Fluid::write::GetMaterialsFile $write_const_law $include_modelpart_name]
 }
 proc Fluid::write::GetMaterialsFile { {write_const_law True} {include_modelpart_name True} } {
     set model_part_name ""
     if {[write::isBooleanTrue $include_modelpart_name]} {set model_part_name [GetAttribute model_part_name]}
-    return [write::getPropertiesJson [GetAttribute parts_un] $write_const_law $model_part_name]
+    set parts [write::getPropertiesJson [GetAttribute parts_un] $write_const_law $model_part_name]
+    set base [dict create model_part_name [GetAttribute model_part_name] properties_id 0 Material null]
+    set old_list [dict get $parts properties]
+    set new_list [concat [list $base] $old_list]
+    set result [dict create properties $new_list]
+    return $result
 }
 
 proc ::Fluid::write::Validate {} {
     set err ""
     set root [customlib::GetBaseRoot]
-
+    
     # Check only 1 part in Parts
     set xp1 "[spdAux::getRoute [GetAttribute parts_un]]/group"
     if {[llength [$root selectNodes $xp1]] ne 1} {
         set err "You must set one part in Parts.\n"
     }
 
+    # if the user has selected MPI, check that the write is set to entities
+    if {[write::getValue ParallelType] eq "MPI"} {
+        if {[GetAttribute write_mdpa_mode] ne "entities"} {
+            set err "You must set the write mode to entities when using MPI.\nCheck the Preferences window.\n"
+        }
+    }
+
     # Check closed volume
     #if {[CheckClosedVolume] ne 1} {
-    #    append err "Check boundary conditions."
-    #}
+        #    append err "Check boundary conditions."
+        #}
     return $err
 }
 
@@ -126,7 +184,7 @@ proc ::Fluid::write::getFluidModelPartFilename { } {
 proc ::Fluid::write::writeBoundaryConditions { } {
     variable FluidConditionMap
     variable last_condition_iterator
-
+    
     # Prepare the groups to print
     set BCUN [GetAttribute conditions_un]
     set root [customlib::GetBaseRoot]
@@ -146,7 +204,7 @@ proc ::Fluid::write::writeBoundaryConditions { } {
     set skin_group_name "_HIDDEN__SKIN_"
     if {[GiD_Groups exists $skin_group_name]} {GiD_Groups delete $skin_group_name}
     spdAux::MergeGroups $skin_group_name $groups
-
+    
     # Write the conditions
     if {$::Model::SpatialDimension eq "3D"} {
         set kname SurfaceCondition3D3N
@@ -156,7 +214,7 @@ proc ::Fluid::write::writeBoundaryConditions { } {
         set nnodes 2
     }
     set last_condition_iterator [write::writeGroupConditionByUniqueId $skin_group_name $kname $nnodes 0 $::Fluid::write::FluidConditionMap]
-
+    
     # Clean
     GiD_Groups delete $skin_group_name
 }
@@ -175,7 +233,7 @@ proc ::Fluid::write::writeMeshes { } {
 }
 
 proc ::Fluid::write::writeConditionsMesh { } {
-
+    
     set root [customlib::GetBaseRoot]
     set xp1 "[spdAux::getRoute [GetAttribute conditions_un]]/condition/group"
     set grouped_conditions [list ]
@@ -199,7 +257,7 @@ proc ::Fluid::write::writeConditionsMesh { } {
             }
         }
     }
-
+    
     foreach condid $grouped_conditions {
         set xp "[spdAux::getRoute [GetAttribute conditions_un]]/condition\[@n='$condid'\]/group"
         set groups_dict [dict create ]
@@ -213,11 +271,11 @@ proc ::Fluid::write::writeConditionsMesh { } {
 
 # Overwrite this function to print something at the end of the mdpa
 proc ::Fluid::write::writeCustomBlocks { } {
-
+    
 }
 
 proc ::Fluid::write::InitConditionsMap { {map "" } } {
-
+    
     variable FluidConditionMap
     if {$map eq ""} {
         set FluidConditionMap [objarray new intarray [expr [GiD_Info Mesh MaxNumElements] +1] 0]
@@ -226,7 +284,7 @@ proc ::Fluid::write::InitConditionsMap { {map "" } } {
     }
 }
 proc ::Fluid::write::FreeConditionsMap { } {
-
+    
     variable FluidConditionMap
     unset FluidConditionMap
 }