Merge branch 'hannes-philipp' of git.gfz-potsdam.de:naaice/tug into hannes-philipp

.gitlab-ci.yml

@@ -4,6 +4,7 @@ stages:
     - build
     - test
     - static_analyze
+    - doc
 
 build_release:
   stage: build
@@ -22,6 +23,23 @@ test:
     script:
         - ./build/test/testTug
 
+pages:
+  stage: doc
+  image: python:slim
+  before_script:
+    - apt-get update && apt-get install --no-install-recommends -y graphviz imagemagick doxygen make
+    - pip install --upgrade pip && pip install Sphinx Pillow breathe sphinx-rtd-theme
+    - mkdir public
+  script:
+    - pushd docs_sphinx
+    - make html
+    - popd && mv docs_sphinx/_build/html/* public/
+  artifacts:
+    paths:
+      - public
+  rules:
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+
 lint:
   stage: static_analyze
   before_script:

.readthedocs.yaml

@@ -1,32 +0,0 @@
-# .readthedocs.yaml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
-version: 2
-
-# Set the OS, Python version and other tools you might need
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.11"
-    # You can also specify other tool versions:
-    # nodejs: "19"
-    # rust: "1.64"
-    # golang: "1.19"
-
-# Build documentation in the "docs/" directory with Sphinx
-sphinx:
-   configuration: docs_sphinx/conf.py
-
-# Optionally build your docs in additional formats such as PDF and ePub
-formats:
-   - pdf
-#    - epub
-
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-python:
-   install:
-   - requirements: docs_sphinx/requirements.txt

CMakeLists.txt

@@ -7,7 +7,8 @@ set(CMAKE_CXX_STANDARD 17)
 
 find_package(Eigen3 REQUIRED NO_MODULE)
 find_package(OpenMP)
-find_package(easy_profiler)
+# find_package(easy_profiler)
+# option(EASY_OPTION_LOG "Verbose easy_profiler" 1)
 
 ## SET(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -O2 -mfma")
 option(TUG_USE_OPENMP "Compile with OpenMP support" ON)

doc/ADI_scheme.org

@@ -1,6 +1,7 @@
 #+TITLE: Finite Difference Schemes for the numerical solution of heterogeneous diffusion equation in 2D
 #+LaTeX_CLASS_OPTIONS: [a4paper,10pt]
 #+LATEX_HEADER: \usepackage{fullpage}
+#+LATEX_HEADER: \usepackage{charter}
 #+LATEX_HEADER: \usepackage{amsmath, systeme, cancel, xcolor}
 #+OPTIONS: toc:nil
 

doc/ValidationHetDiff.org

@@ -1,12 +1,12 @@
-#+TITLE: 2D Validation Examples
+#+TITLE: Validation Examples for 2D Heterogeneous Diffusion
 #+AUTHOR: MDL <delucia@gfz-potsdam.de>
-#+DATE: 2023-07-31
+#+DATE: 2023-08-26
 #+STARTUP: inlineimages
 #+LATEX_CLASS_OPTIONS: [a4paper,9pt]
 #+LATEX_HEADER: \usepackage{fullpage}
 #+LATEX_HEADER: \usepackage{amsmath, systeme}
 #+LATEX_HEADER: \usepackage{graphicx}
-#+LATEX_HEADER: \usepackage{}
+#+LATEX_HEADER: \usepackage{charter}
 #+OPTIONS: toc:nil
 
 
@@ -38,7 +38,7 @@ constant in 4 quadrants:
 The relevant part of the R script used to produce these results is
 presented in listing 1; the whole script is at [[file:scripts/HetDiff.R]].
 A visualization of the output of the reference simulation is given in
-figure [[#fig:1][1]].
+figure [[fig:1][1]].
 
 Note: all results from this script are stored in the =outc= matrix by
 the =deSolve= function. I stored a different version into
@@ -47,6 +47,7 @@ for each time step including initial conditions) and 121 rows, one for
 each domain element, with no headers.
 
 #+caption: Result of ReacTran/deSolve solution of the above problem at 4
+#+name: fig:1
 [[./images/deSolve_AlphaHet1.png]]
 
 

docs_sphinx/index.rst

@@ -5,12 +5,26 @@
 
 Welcome to Tug's documentation!
 ===============================
+
 Welcome to the documentation of the TUG project, a simulation program
-for solving one- and two-dimensional diffusion problems with heterogeneous diffusion coefficients, more 
+for solving transport equations in one- and two-dimensional uniform
-generally, for solving the following differential equation
+grids using cell centered finite differences.
+
+---------
+Diffusion
+---------
+
+TUG can solve diffusion problems with heterogeneous and anisotropic
+diffusion coefficients. The partial differential equation expressing
+diffusion reads:
 
 .. math::
-   \frac{\partial C}{\partial t} = \alpha_x \frac{\partial^2 C}{\partial x^2} + \alpha_y \frac{\partial^2 C}{\partial y^2}.
+   \frac{\partial C}{\partial t} =  \nabla \cdot \left[ \mathbf{\alpha} \nabla C \right]
+
+In 2D, the equation reads:
+   
+.. math::
+   \frac{\partial C}{\partial t} =  \frac{\partial}{\partial x}\left[ \alpha_x \frac{\partial C}{\partial x}\right] + \frac{\partial}{\partial y}\left[ \alpha_y \frac{\partial C}{\partial y}\right]
 
 .. toctree::
    :maxdepth: 2

examples/CMakeLists.txt

@@ -4,6 +4,7 @@ add_executable(BTCS_1D_proto_example BTCS_1D_proto_example.cpp)
 add_executable(BTCS_2D_proto_example BTCS_2D_proto_example.cpp)
 add_executable(reference-FTCS_2D_closed reference-FTCS_2D_closed.cpp)
 add_executable(profiling_openmp profiling_openmp.cpp)
+
 target_link_libraries(FTCS_1D_proto_example tug)
 target_link_libraries(FTCS_2D_proto_example tug)
 target_link_libraries(BTCS_1D_proto_example tug)

src/BTCSv2.cpp

@@ -278,10 +278,10 @@ static VectorXd EigenLUAlgorithm(SparseMatrix<double> &A, VectorXd &b) {
 static VectorXd ThomasAlgorithm(SparseMatrix<double> &A, VectorXd &b) {
     uint32_t n = b.size();
 
-    VectorXd a_diag(n);
+    Eigen::VectorXd a_diag(n);
-    VectorXd b_diag(n);
+    Eigen::VectorXd b_diag(n);
-    VectorXd c_diag(n);
+    Eigen::VectorXd c_diag(n);
-    VectorXd x_vec = b;
+    Eigen::VectorXd x_vec = b;
 
     // Fill diagonals vectors
     b_diag[0] = A.coeff(0, 0);
@@ -367,7 +367,6 @@ static void BTCS_2D(Grid &grid, Boundary &bc, double timestep, VectorXd (*solver
     SparseMatrix<double> A;
     VectorXd b;
 
-    // const MatrixXd &alphaX = grid.getAlphaX(); // TODO check if this helps performance
     MatrixXd alphaX = grid.getAlphaX();
     MatrixXd alphaY = grid.getAlphaY();
     vector<BoundaryElement> bcLeft = bc.getBoundarySide(BC_SIDE_LEFT);
@@ -385,7 +384,7 @@ static void BTCS_2D(Grid &grid, Boundary &bc, double timestep, VectorXd (*solver
         b = createSolutionVector(concentrations, alphaX, alphaY, bcLeft, bcRight, 
                                     bcTop, bcBottom, colMax, i, sx, sy);
         
-        SparseLU<SparseMatrix<double>> solver; // TODO what is this?
+        SparseLU<SparseMatrix<double>> solver; 
 
         row_t1 = solverFunc(A, b);
         
@@ -417,10 +416,10 @@ static void BTCS_2D(Grid &grid, Boundary &bc, double timestep, VectorXd (*solver
 
 // entry point for EigenLU solver; differentiate between 1D and 2D grid
 static void BTCS_LU(Grid &grid, Boundary &bc, double timestep, int numThreads) {
-    if (grid.getDim() == 2) {
+    if (grid.getDim() == 1) {
-        BTCS_2D(grid, bc, timestep, EigenLUAlgorithm, numThreads);
-    } else if (grid.getDim() == 1) {
         BTCS_1D(grid, bc, timestep, EigenLUAlgorithm);
+    } else if (grid.getDim() == 2) {
+        BTCS_2D(grid, bc, timestep, EigenLUAlgorithm, numThreads);
     } else {
         throw_invalid_argument("Error: Only 1- and 2-dimensional grids are defined!");
     }
@@ -428,10 +427,10 @@ static void BTCS_LU(Grid &grid, Boundary &bc, double timestep, int numThreads) {
 
 // entry point for Thomas algorithm solver; differentiate 1D and 2D grid
 static void BTCS_Thomas(Grid &grid, Boundary &bc, double timestep, int numThreads) {
-    if (grid.getDim() == 2) {
+    if (grid.getDim() == 1) {
-        BTCS_2D(grid, bc, timestep, ThomasAlgorithm, numThreads);
-    } else if (grid.getDim() == 1) {
         BTCS_1D(grid, bc, timestep, ThomasAlgorithm);
+    } else if (grid.getDim() == 2) {
+        BTCS_2D(grid, bc, timestep, ThomasAlgorithm, numThreads);
     } else {
         throw_invalid_argument("Error: Only 1- and 2-dimensional grids are defined!");
     }