Revert "Merge branch 'master' into PfemFluid/add-constitutive-laws"

This reverts commit 0b7dd9e.
KratosMultiphysics · May 1, 2020 · 3df67a3 · 3df67a3
1 parent 0b7dd9e
commit 3df67a3
Show file tree

Hide file tree

Showing 496 changed files with 61,974 additions and 17,164 deletions.
diff --git a/.github/workflows/build_docker_image_wheelbuilder_linux.yml b/.github/workflows/build_docker_image_wheelbuilder_linux.yml
diff --git a/.github/workflows/build_docker_image_wheelbuilder_windows.yml b/.github/workflows/build_docker_image_wheelbuilder_windows.yml
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -101,13 +101,11 @@ jobs:
         set KRATOS_APP_DIR=applications
 
         set KRATOS_APPLICATIONS=
-        set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\ConvectionDiffusionApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\FluidDynamicsApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\MeshingApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\MeshMovingApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\EigenSolversApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\StructuralMechanicsApplication;
-        set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\ChimeraApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\IgaApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\ParticleMechanicsApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\MappingApplication;
@@ -121,7 +119,8 @@ jobs:
           -G"Visual Studio 16 2019"                          ^
           -H"%KRATOS_SOURCE%"                                ^
           -B"%KRATOS_BUILD%\%KRATOS_BUILD_TYPE%"             ^
-          -DBOOST_ROOT="%BOOST_ROOT_1_72_0%"                 ^
+          -DBOOST_ROOT="%BOOST_ROOT%"                        ^
+          -DINCLUDE_FEAST=OFF                                ^
           -DINSTALL_RUNKRATOS=OFF                            ^
           -DCMAKE_CXX_FLAGS="/Od"                            ^
           -DUSE_COTIRE=ON                                    || goto :error

diff --git a/.github/workflows/configure.sh b/.github/workflows/configure.sh
@@ -20,7 +20,6 @@ export PYTHON_EXECUTABLE="/usr/bin/python3.6"
 export KRATOS_INSTALL_PYTHON_USING_LINKS=ON
 
 # Set applications to compile
-add_app ${KRATOS_APP_DIR}/ConvectionDiffusionApplication;
 add_app ${KRATOS_APP_DIR}/ExternalSolversApplication;
 add_app ${KRATOS_APP_DIR}/EigenSolversApplication;
 add_app ${KRATOS_APP_DIR}/StructuralMechanicsApplication;
@@ -42,7 +41,6 @@ add_app ${KRATOS_APP_DIR}/HDF5Application;
 add_app ${KRATOS_APP_DIR}/ContactStructuralMechanicsApplication;
 add_app ${KRATOS_APP_DIR}/IgaApplication;
 add_app ${KRATOS_APP_DIR}/ParticleMechanicsApplication;
-add_app ${KRATOS_APP_DIR}/ChimeraApplication;
 
 # Clean
 clear
@@ -75,3 +73,4 @@ ${KRATOS_CMAKE_OPTIONS_FLAGS} \
 # Buid
 cmake --build "${KRATOS_BUILD}/${KRATOS_BUILD_TYPE}" --target all_unity    -- -j1 && \
 cmake --build "${KRATOS_BUILD}/${KRATOS_BUILD_TYPE}" --target install/fast -- -j1
+
diff --git a/.github/workflows/nightly_build.yml b/.github/workflows/nightly_build.yml
@@ -78,7 +78,6 @@ jobs:
         set KRATOS_APP_DIR=applications
 
         set KRATOS_APPLICATIONS=
-        set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\ConvectionDiffusionApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\FluidDynamicsApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\StructuralMechanicsApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\ContactStructuralMechanicsApplication;
@@ -90,9 +89,6 @@ jobs:
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\EigenSolversApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\IgaApplication;
         set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\ParticleMechanicsApplication;
-        set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\ChimeraApplication;
-        set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\MappingApplication;
-        set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\CoSimulationApplication;
 
         del /F /Q "%KRATOS_BUILD%\%KRATOS_BUILD_TYPE%\cmake_install.cmake"
         del /F /Q "%KRATOS_BUILD%\%KRATOS_BUILD_TYPE%\CMakeCache.txt"
@@ -102,7 +98,8 @@ jobs:
           -G"Visual Studio 16 2019"                          ^
           -H"%KRATOS_SOURCE%"                                ^
           -B"%KRATOS_BUILD%\%KRATOS_BUILD_TYPE%"             ^
-          -DBOOST_ROOT="%BOOST_ROOT_1_72_0%"                 ^
+          -DBOOST_ROOT="%BOOST_ROOT%"                        ^
+          -DINCLUDE_FEAST=OFF                                ^
           -DINSTALL_RUNKRATOS=OFF                            ^
           -DCMAKE_CXX_FLAGS="/Od"                            ^
           -DUSE_COTIRE=ON                                    || goto :error

diff --git a/INSTALL.md b/INSTALL.md
@@ -1,22 +1,21 @@
 # Contents
-- [Contents](#contents)
-  - [Basic Configuration](#basic-configuration)
-  - [Adding Applications](#adding-applications)
-  - [Adding Kratos to Path](#adding-kratos-to-path)
-  - [Examples](#examples)
-    - [Linux](#linux)
-    - [Windows](#windows)
-    - [MacOS](#macos)
-  - [Advanced Configuration](#advanced-configuration)
-    - [Building Environment](#building-environment)
-    - [Common Flags](#common-flags)
-    - [Compilation Performance](#compilation-performance)
-    - [Parallelism](#parallelism)
-    - [Logging](#logging)
-    - [External libraries](#external-libraries)
-      - [Metis](#metis)
-      - [Trilinos](#trilinos)
-  - [Applications](#applications)
+* [Basic Configuration](#basic-configuration)
+* [Adding Applications](#basic-configuration)
+* [Adding Kratos to Path](#adding-kratos-to-path)
+* [Examples](#examples)
+  * [Linux](#linux)
+  * [Windows](#windows)
+  * [MacOS](#macos)
+* [Advanced Configuration](#advanced-configuration)
+  * [Building Environment](#building-environments)
+  * [Common Flags](#common-flags)
+  * [Compilation Performance](#compilation-performance)
+  * [Parallelism](#parallelism)
+  * [External Libraries](#external-libraries)
+    * [Feast](#feast)
+    * [Metis](#metis)
+    * [Trilinos](#trilinos)
+* [Applications](#applications)
 
 
 ## Basic Configuration
@@ -316,6 +315,11 @@ Enables or Disables(default) the modules and code for mpi. This option is needed
 Enables colored output of the Logger. If switched on, e.g. warning level messages will be printed in yellow to the terminal. Please notice that colored output is not supported by all terminals.
 
 ### External libraries
+#### Feast
+`-DINCLUDE_FEAST`
+
+Enables or Disables(default) the use of FEAST
+
 #### Metis
 
 `-DUSE_METIS_5=ON/OFF`

diff --git a/applications/CableNetApplication/cable_net_application_variables.h b/applications/CableNetApplication/cable_net_application_variables.h
@@ -19,8 +19,8 @@
 
 // Project includes
 #include "includes/define.h"
-#include "containers/variable.h"
-#include "includes/ublas_interface.h"
+#include "includes/variables.h"
+#include "includes/kratos_application.h"
 
 namespace Kratos
 {

diff --git a/applications/CableNetApplication/custom_elements/empirical_spring.cpp b/applications/CableNetApplication/custom_elements/empirical_spring.cpp
@@ -16,11 +16,11 @@
 
 // Project includes
 #include "custom_elements/empirical_spring.hpp"
+#include "includes/define.h"
 #include "structural_mechanics_application_variables.h"
 #include "cable_net_application_variables.h"
 #include "includes/checks.h"
 #include "custom_utilities/structural_mechanics_element_utilities.h"
-#include "includes/variables.h"
 
 
 namespace Kratos {
@@ -53,7 +53,7 @@ EmpiricalSpringElement3D2N::Create(IndexType NewId, GeometryType::Pointer pGeom,
 EmpiricalSpringElement3D2N::~EmpiricalSpringElement3D2N() {}
 
 void EmpiricalSpringElement3D2N::EquationIdVector(EquationIdVectorType& rResult,
-                                                  const ProcessInfo& rCurrentProcessInfo) const
+                                        ProcessInfo& rCurrentProcessInfo)
 {
 
     if (rResult.size() != msLocalSize) {
@@ -70,7 +70,7 @@ void EmpiricalSpringElement3D2N::EquationIdVector(EquationIdVectorType& rResult,
     }
 }
 void EmpiricalSpringElement3D2N::GetDofList(DofsVectorType& rElementalDofList,
-                                            const ProcessInfo& rCurrentProcessInfo) const
+                                  ProcessInfo& rCurrentProcessInfo)
 {
 
     if (rElementalDofList.size() != msLocalSize) {
@@ -90,7 +90,7 @@ void EmpiricalSpringElement3D2N::GetDofList(DofsVectorType& rElementalDofList,
 BoundedMatrix<double, EmpiricalSpringElement3D2N::msLocalSize,
 EmpiricalSpringElement3D2N::msLocalSize>
 EmpiricalSpringElement3D2N::CreateElementStiffnessMatrix(
-    const ProcessInfo& rCurrentProcessInfo)
+    ProcessInfo& rCurrentProcessInfo)
 {
     BoundedMatrix<double, msLocalSize, msLocalSize> stiffness_matrix =
         ZeroMatrix(msLocalSize, msLocalSize);
@@ -128,8 +128,9 @@ double EmpiricalSpringElement3D2N::EvaluatePolynomialFirstDerivative(const Vecto
 }
 
 
-void EmpiricalSpringElement3D2N::GetValuesVector(Vector& rValues, int Step) const
+void EmpiricalSpringElement3D2N::GetValuesVector(Vector& rValues, int Step)
 {
+
     KRATOS_TRY
     if (rValues.size() != msLocalSize) {
         rValues.resize(msLocalSize, false);
@@ -147,7 +148,7 @@ void EmpiricalSpringElement3D2N::GetValuesVector(Vector& rValues, int Step) cons
     KRATOS_CATCH("")
 }
 
-void EmpiricalSpringElement3D2N::GetFirstDerivativesVector(Vector& rValues, int Step) const
+void EmpiricalSpringElement3D2N::GetFirstDerivativesVector(Vector& rValues, int Step)
 {
 
     KRATOS_TRY
@@ -167,7 +168,7 @@ void EmpiricalSpringElement3D2N::GetFirstDerivativesVector(Vector& rValues, int
     KRATOS_CATCH("")
 }
 
-void EmpiricalSpringElement3D2N::GetSecondDerivativesVector(Vector& rValues, int Step) const
+void EmpiricalSpringElement3D2N::GetSecondDerivativesVector(Vector& rValues, int Step)
 {
 
     KRATOS_TRY
@@ -189,8 +190,8 @@ void EmpiricalSpringElement3D2N::GetSecondDerivativesVector(Vector& rValues, int
 }
 
 void EmpiricalSpringElement3D2N::CalculateLocalSystem(MatrixType& rLeftHandSideMatrix,
-                                                      VectorType& rRightHandSideVector,
-                                                      const ProcessInfo& rCurrentProcessInfo)
+        VectorType& rRightHandSideVector,
+        ProcessInfo& rCurrentProcessInfo)
 {
     KRATOS_TRY;
     CalculateRightHandSide(rRightHandSideVector,rCurrentProcessInfo);
@@ -199,7 +200,7 @@ void EmpiricalSpringElement3D2N::CalculateLocalSystem(MatrixType& rLeftHandSideM
 }
 
 void EmpiricalSpringElement3D2N::CalculateRightHandSide(
-    VectorType& rRightHandSideVector, const ProcessInfo& rCurrentProcessInfo)
+    VectorType& rRightHandSideVector, ProcessInfo& rCurrentProcessInfo)
 {
 
     KRATOS_TRY
@@ -219,7 +220,7 @@ void EmpiricalSpringElement3D2N::CalculateRightHandSide(
 }
 
 void EmpiricalSpringElement3D2N::CalculateLeftHandSide(MatrixType& rLeftHandSideMatrix,
-        const ProcessInfo& rCurrentProcessInfo)
+        ProcessInfo& rCurrentProcessInfo)
 {
 
     KRATOS_TRY;
@@ -231,7 +232,7 @@ void EmpiricalSpringElement3D2N::CalculateLeftHandSide(MatrixType& rLeftHandSide
     KRATOS_CATCH("")
 }
 
-int EmpiricalSpringElement3D2N::Check(const ProcessInfo& rCurrentProcessInfo) const
+int EmpiricalSpringElement3D2N::Check(const ProcessInfo& rCurrentProcessInfo)
 {
     KRATOS_TRY
     const double numerical_limit = std::numeric_limits<double>::epsilon();
@@ -249,7 +250,7 @@ int EmpiricalSpringElement3D2N::Check(const ProcessInfo& rCurrentProcessInfo) co
 
     // Check that the element's nodes contain all required SolutionStepData and Degrees of freedom
     for (IndexType i = 0; i < number_of_nodes; ++i) {
-        const NodeType& rnode = GetGeometry()[i];
+        NodeType& rnode = GetGeometry()[i];
         KRATOS_CHECK_VARIABLE_IN_NODAL_DATA(DISPLACEMENT, rnode);
 
         KRATOS_CHECK_DOF_IN_NODE(DISPLACEMENT_X, rnode);
@@ -444,7 +445,7 @@ void EmpiricalSpringElement3D2N::CalculateLumpedMassVector(VectorType& rMassVect
 
 void EmpiricalSpringElement3D2N::CalculateMassMatrix(
     MatrixType& rMassMatrix,
-    const ProcessInfo& rCurrentProcessInfo
+    ProcessInfo& rCurrentProcessInfo
 )
 {
     KRATOS_TRY
@@ -468,7 +469,7 @@ void EmpiricalSpringElement3D2N::CalculateMassMatrix(
 }
 
 void EmpiricalSpringElement3D2N::CalculateDampingMatrix(
-    MatrixType& rDampingMatrix, const ProcessInfo& rCurrentProcessInfo)
+    MatrixType& rDampingMatrix, ProcessInfo& rCurrentProcessInfo)
 {
     StructuralMechanicsElementUtilities::CalculateRayleighDampingMatrix(
         *this,
@@ -481,7 +482,7 @@ void EmpiricalSpringElement3D2N::CalculateDampingMatrix(
 void EmpiricalSpringElement3D2N::AddExplicitContribution(
     const VectorType& rRHSVector,
     const Variable<VectorType>& rRHSVariable,
-    const Variable<double >& rDestinationVariable,
+    Variable<double >& rDestinationVariable,
     const ProcessInfo& rCurrentProcessInfo
 )
 {
@@ -507,7 +508,7 @@ void EmpiricalSpringElement3D2N::AddExplicitContribution(
 
 void EmpiricalSpringElement3D2N::AddExplicitContribution(
     const VectorType& rRHSVector, const Variable<VectorType>& rRHSVariable,
-    const Variable<array_1d<double, 3>>& rDestinationVariable,
+    Variable<array_1d<double, 3>>& rDestinationVariable,
     const ProcessInfo& rCurrentProcessInfo
 )
 {