Merge branch 'vale-fixes' into 'master'

[vale] Fixed all issues See merge request ogs/ogs!4686
ufz · Jul 21, 2023 · ef05d75 · ef05d75
2 parents 4595e22 + e0e9794
commit ef05d75
Show file tree

Hide file tree

Showing 58 changed files with 420 additions and 307 deletions.
diff --git a/.vale.ini b/.vale.ini
@@ -9,7 +9,7 @@ Packages = Hugo
 [*.md]
 BasedOnStyles = Vale, write-good, ogs
 Vale.Spelling = None
-write-good.ThereIs = suggestion
+write-good.ThereIs = None
 write-good.Passive = None
 write-good.TooWordy = None
 write-good.Weasel = None
@@ -21,7 +21,10 @@ TokenIgnores = \
 ; (\\ref\s\S+(\s"\S*")?), \
 ; (\\subpage\s\S*), \
 ; (\\copydoc\s\S*), \
-(\$+[^\n$]+\$+), \
 (\$[^\n$]+\$), \
 (\\\S*|\{\S*\}), \
-(\w*\set\sal)
+(\w*\set\sal), \
+({{<\s?(rel)?ref (.*)>}})
+
+# https://regex101.com/r/QWLhgT/1 helped me generating this one:
+BlockIgnores = (?s) *(\$\$.*?\$\$)
diff --git a/Documentation/.vale/.vale-config/0-Hugo.ini b/Documentation/.vale/.vale-config/0-Hugo.ini
@@ -0,0 +1,8 @@
+[*.md]
+# Exclude `{{< ... >}}`, `{{% ... %}}`, [Who]({{< ... >}})
+TokenIgnores = ({{[%<] .* [%>]}}.*?{{[%<] ?/.* [%>]}}), \
+(\[.+\]\({{< .+ >}}\))
+
+# Exclude `{{< myshortcode `This is some <b>HTML</b>, ... >}}`
+BlockIgnores = (?sm)^({{[%<] [^{]*? [%>]}})\n$, \
+(?s) *({{< highlight [^>]* ?>}}.*?{{< ?/ ?highlight >}})
diff --git a/Documentation/.vale/Vocab/ogs/accept.txt b/Documentation/.vale/Vocab/ogs/accept.txt
@@ -1,9 +1,13 @@
+Alcolea
 Algolia
 Aluminol
 Alves
 Atteia
 Autolinks
+BC[s?]
 Beier
+BGR[a?]
+BHE[s?]
 Bincrafters
 biokinetic
 Biot
@@ -14,6 +18,7 @@ Bruns
 CLion
 Dalen
 Degener
+DEM[s?]
 devguide
 Diao
 Diersch
@@ -29,34 +34,37 @@ Eskilson
 Everton
 Fancybox
 FancyBox
+FEFLOW
 Feldspars
 fmt
 Forchheimer
 Fortran
 Francesco
 frontmatter
+Galerkin
 Genuchten
 Geoenergy
-Galerkin
 Giraldo
 gml
 GML
 Gmsh
+Gnielinski
 Goswami
 Guo
 Heidemann
 Homebrew
 Horner
-HTTPS
 IPhreeqc
 ipynb
 ipyvtklink
 Jacobian
 Johannsen
 Jong
 Jupyter
+Jupytext
 Juwels
 Kinzelbach
+Kitware
 Kolditz
 Laloui
 Langergraber
@@ -68,9 +76,11 @@ Massmann
 Matplotlib
 meshio
 METIS
+MFront
 Mikelic
 Mises
 MODFLOW
+MTest
 nbconvert
 nbdime
 Netbeans
@@ -87,7 +97,9 @@ parameteri[zs]ation
 ParaView
 Parisio
 partmesh
+PDE[s?]
 Péclet
+PETSc
 PHREEQC
 Pinheiro
 Prandtl
@@ -98,6 +110,7 @@ pvpython
 PVTU
 Quadro
 Quirijn
+Ramey
 recondensation
 relref
 Revista
@@ -107,13 +120,16 @@ Rossendorf
 Ruehaak
 Scheidegger
 semianalytical
+SGrid
 Shao
 shortcode
 Snakemake
 Srivastava
+ST[s?]
 Stauffer
 Stauffer
 stdout
+stepping[s?]
 storativity
 Tarok
 Taucha
@@ -122,16 +138,19 @@ TESPy
 Theis
 Thuringia
 Thuringian
+TODO[s?]
 Ucar
 Unlicense
 Unstrut
 Vogel
 Vogels
 vtkdiff
-VTU
+VTK[s?]
+VTUinterface
 Witte
 Xcode
 Xeon
 XPath
 Youngs
 Zenodo
+zlib
diff --git a/Documentation/.vale/Vocab/ogs/ignore.txt b/Documentation/.vale/Vocab/ogs/ignore.txt
@@ -54,3 +54,9 @@ thermomechanics
 undeformed
 voxel
 wellbore
+expansivity
+simplices
+orthotropic
+tetrahedralization
+cmake
+ctest
diff --git a/scripts/ci/jobs/build-docs.yml b/scripts/ci/jobs/build-docs.yml
@@ -99,7 +99,7 @@ check docs links:
  build/docs
 
 spell check docs:
- image: registry.gitlab.com/gitlab-org/gitlab-docs/lint-markdown:alpine-3.15-vale-2.16.1-markdownlint-0.31.1
+ image: registry.gitlab.com/gitlab-org/gitlab-docs/lint-markdown:alpine-3.18-vale-2.27.0-markdownlint-0.35.0-markdownlint2-0.8.1
  stage: check
  needs: []
  variables:

diff --git a/scripts/ci/jobs/code-quality.yml b/scripts/ci/jobs/code-quality.yml
@@ -7,8 +7,7 @@ cppcheck:
  - cd build
  script:
  - >
- cmake .. -G Ninja -DCMAKE_BUILD_TYPE=Release -DOGS_USE_CONAN=OFF
- -DOGS_BUILD_UTILS=OFF
+ cmake .. -G Ninja -DCMAKE_BUILD_TYPE=Release -DOGS_BUILD_UTILS=OFF
  -DOGS_USE_UNITY_BUILDS=OFF -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
  - bash cppcheck.sh
  artifacts:

diff --git a/scripts/cmake/CppCheck.cmake b/scripts/cmake/CppCheck.cmake
@@ -9,10 +9,13 @@ elseif(DEFINED CMAKE_BUILD_PARALLEL_LEVEL)
  set(CPPCHECK_PARALLEL ${CMAKE_BUILD_PARALLEL_LEVEL})
 endif()
 if(DEFINED CPM_SOURCE_CACHE)
- set(_cpp_check_ingore "-i${CPM_SOURCE_CACHE}")
+ set(_cpm_dir ${CPM_SOURCE_CACHE})
+elseif(DEFINED ENV{CPM_SOURCE_CACHE})
+ set(_cpm_dir $ENV{CPM_SOURCE_CACHE})
 else()
- set(_cpp_check_ingore "-i${PROJECT_BINARY_DIR}/_deps")
+ set(_cpm_dir ${PROJECT_BINARY_DIR}/_deps)
 endif()
+set(_last_sed_expression [['x;${s/,$//;p;x;};1d']])
 
 configure_file(
  ${PROJECT_SOURCE_DIR}/scripts/test/cppcheck.in.sh
@@ -25,13 +28,6 @@ endif()
 
 add_custom_target(
  cppcheck
- COMMAND
- ${CPPCHECK_TOOL_PATH}
- --project=${PROJECT_BINARY_DIR}/compile_commands.json --language=c++
- --std=c++20 --enable=all --inconclusive ${CPPCHECK_THREADS} -i
- ${PROJECT_BINARY_DIR}/CMakeFiles -i ${PROJECT_BINARY_DIR}/_deps -i
- ${PROJECT_SOURCE_DIR}/ThirdParty -i
- ${PROJECT_SOURCE_DIR}/Applications/DataExplorer -i
- ${PROJECT_SOURCE_DIR}/Tests --xml --xml-version=2
- --output-file=${PROJECT_BINARY_DIR}/cppcheck.log ${PROJECT_SOURCE_DIR}
+ COMMAND ${BASH_TOOL_PATH} cppcheck.sh
+ WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
 )
diff --git a/scripts/test/cppcheck.in.sh b/scripts/test/cppcheck.in.sh
@@ -5,15 +5,15 @@ OUTPUT_FILE=${PROJECT_BINARY_DIR}/cppcheck.json
 ${CPPCHECK_TOOL_PATH} \
  --project=${PROJECT_BINARY_DIR}/compile_commands.json \
  --language=c++ \
- --std=c++20 \
+ --std=c++${CMAKE_CXX_STANDARD} \
  --enable=all \
  --inconclusive \
  -j ${CPPCHECK_PARALLEL} \
- ${_cpp_check_ingore} \
  --inline-suppr \
- --suppress=*:*/usr/local\* \
- --suppress=*:*cpm\* \
- --suppress=*:*Tests\* \
+ -i ${_cpm_dir} --suppress=*:${_cpm_dir}/* \
+ -i ${PROJECT_SOURCE_DIR}/ThirdParty --suppress=*:${PROJECT_SOURCE_DIR}/ThirdParty* \
+ -i ${PROJECT_SOURCE_DIR}/Tests --suppress=*:*Tests/* \
+ --suppress=missingIncludeSystem \
  --template='{\n "description": "{message}",\n "severity": "info",\n "location": {\n "path": "{file}",\n "lines": {\n "begin": {line}\n }\n }\n},' \
  --output-file="$OUTPUT_FILE.tmp"
 
@@ -24,15 +24,21 @@ $(
  `: strip source code absolute path` \
  sed 's|${PROJECT_SOURCE_DIR}/||' | \
  `: escape strings` \
- sed 's/string literal "\(.*\)" to/string literal \\"\1\\" to/g' | \
- `: remove last comma` \
- sed '$s/,$//'
+ sed 's/string literal "\(.*\)" to/string literal \\"\1\\" to/g'
 )
 ]
 EOF
 
+cat <<EOF >"$OUTPUT_FILE"
+$(
+ cat "$OUTPUT_FILE" | \
+ `: remove last comma` \
+ sed ${_last_sed_expression}
+)
+EOF
+
 rm "$OUTPUT_FILE.tmp"
 
 if [ -f ${Python_EXECUTABLE} ]; then
-  ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/scripts/test/cppcheck_gen_hashes.py "$OUTPUT_FILE"
+ ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/scripts/test/cppcheck_gen_hashes.py "$OUTPUT_FILE"
 fi
diff --git a/web/content/docs/benchmarks/elliptic/elliptic-neumann/index.md b/web/content/docs/benchmarks/elliptic/elliptic-neumann/index.md
@@ -35,12 +35,22 @@ k\\;{\partial h(x,y) \over \partial n} = 0 &\quad \text{on } (x,y=1) \subset \Ga
 }$$
 
 The solution of this problem is
+
 $$
-\begin{equation}
 h(x,y) = 1 + \sum_{k=1}^\infty A_k \sin\bigg(C_k y\bigg) \sinh\bigg(C_k x\bigg),
-\end{equation}
 $$
-where $C_k = \frac{2k-1}{2} \pi$ and $A_k = 2 \Big/ \Big(C_k^2 \cosh\big(C_k\big)\Big)$.
+
+where
+
+$$
+C_k = \frac{2k-1}{2} \pi
+$$
+
+and
+
+$$
+A_k = 2 \Big/ \Big(C_k^2 \cosh\big(C_k\big)\Big).
+$$
 
 ## Input files
 

diff --git a/web/content/docs/benchmarks/heat-transport-bhe/pipe_flow_EBHE/index.md b/web/content/docs/benchmarks/heat-transport-bhe/pipe_flow_EBHE/index.md
@@ -25,60 +25,73 @@ Figure 1: Single pipe flow model
 
 In Ramey's analytical solution (Ramey et al. (1962)), the outlet temperature of the pipe inside the wellbore can be calculated by,
 
-\begin{equation}
+$$
  T_o(t) = T_{s} + (T_i(t) - T_{s})\exp(-\Delta z/X)
-\end{equation}
+$$
 
 \noindent where, $q$ is the flow rate of the fluid in the wellbore and coefficient $X$ is determined by,
 
-\begin{equation}
+$$
  X = \frac{q\rho_fc_{p,f}(\lambda_{s}+r_pUf(t))}{2\pi r_pU \lambda_{s}}
-\end{equation}
+$$
 
 with dimensionless time $t_D = \frac{\lambda_{s}t}{(\rho_{s}c_{p,s}r_b)}$, the time function $f(t)$ can be calculated by,
 
-\begin{align}
- &f(t) = [0.4063+0.5\ln(t_D)][1+\frac{0.6}{t_D}], & t_D > 1.5
- \\
- &f(t) = 1.1281\sqrt{t_D}(1-0.3\sqrt{t_D}), & t_D \leqslant 1.5
-\end{align}
+<!-- markdownlint-disable reference-links-images -->
 
-\noindent and the overall heat transfer coefficient $U$ is written as follows,
+$$
+ f(t) = [0.4063+0.5\ln(t_D)][1+\frac{0.6}{t_D}], t_D > 1.5
+$$
 
-\begin{equation}
+<!-- markdownlint-enable reference-links-images -->
+
+$$
+ f(t) = 1.1281\sqrt{t_D}(1-0.3\sqrt{t_D}), t_D \leqslant 1.5
+$$
+
+and the overall heat transfer coefficient $U$ is written as follows,
+
+$$
  U = [\frac{r_{pi}+t_{pi}}{r_{pi}h}+(r_{pi}+t_{pi})(\frac{\ln{\frac{r_{pi}+t_{pi}}{r_{pi}}}}{\lambda_{pi}}+\frac{\ln{\frac{r_b}{r_{pi}+t_{pi}}}}{\lambda_{grout}})]^{-1}
-\end{equation}
+$$
 
-\begin{equation}
+$$
  h = \frac{\lambda_f Nu}{2r_{pi}}
-\end{equation}
+$$
 
 The Nusselt number can be determined according to the Gnielinski's equation (Gnielinski et al. (1975)),
 
-\begin{align}
- & Nu = 4.364, & Re < 2300 \\
- & Nu = \frac{\frac{f}{8}(Re - 1000)Pr}{1+12.7\sqrt{\frac{f}{8}}(Pr^{\frac{2}{3}}-1)}, & 2300\leqslant Re < 5 \times 10^6
-\end{align}
+$$
+ Nu = 4.364, Re < 2300
+$$
+
+$$
+ Nu = \frac{\frac{f}{8}(Re - 1000)Pr}{1+12.7\sqrt{\frac{f}{8}}(Pr^{\frac{2}{3}}-1)}, 2300\leqslant Re < 5 \times 10^6
+$$
 
 Pr is the Prandtl number, and the friction factor $f$, is evaluated by Churchill correlation (Churchill et al. (1977)),
 
-\begin{equation}
+$$
  f = \frac{1}{(\frac{1}{[((\frac{8}{Re})^{10}+(\frac{Re}{36500})^{20})]^{1/2}}+[2.21(\ln{\frac{Re}{7}})]^{10})^{1/5}}
-\end{equation}
+$$
 
 The Prandtl and Reynolds number can be calculated as follows,
 
-\begin{align}
- & Pr = \frac{\mu_f c_{p,f}}{\lambda_f}
- & Re = \frac{\rho_f v d_{pi}}{\mu_f}
-\end{align}
-\noindent where, $\mu_f, \rho_f$ and $\lambda_f$ is the fluid viscosity, density and thermal conductivity.
+$$
+ Pr = \frac{\mu_f c_{p,f}}{\lambda_f}
+$$
+
+$$
+ Re = \frac{\rho_f v d_{pi}}{\mu_f}
+$$
+
+where, $\mu_f, \rho_f$ and $\lambda_f$ is the fluid viscosity, density and thermal conductivity.
 
 ## Results and discussion
 
-The outlet temperature change over time was compared against analytical solution and presented in Figure 2. After 30 days, the fluid temperature distribution in the wellbore is shown in Figure 3. The maximum relative error between the numerical model and Ramey's analytical solution is less than 0.15 \%.
+The outlet temperature change over time was compared against analytical solution and presented in Figure 2. After 30 days, the fluid temperature distribution in the wellbore is shown in Figure 3. The maximum relative error between the numerical model and Ramey's analytical solution is less than $0.15\ \\%$.
 
-In numerical model, the outlet temperature at beginning stage is affected by the initial temperature in the pipe inside the wellbore. The initial fluid temperature set in the benchmark means there is water with 20 $^{\circ}$C filled in the wellbore already before injecting water into the wellbore. But in the analytical solution, no initial temperature is set and the temperature keeps equilibrium state at every moment. The impact of initial temperature condition in numerical model is decreasing with the increasing of the operational time as shown in Figure 2.
+In numerical model, the outlet temperature at beginning stage is affected by the initial temperature in the pipe inside the wellbore. The initial fluid temperature set in the benchmark means there is water with $20\ ^{\circ}$C filled in the wellbore already before injecting water into the wellbore. But in the analytical solution, no initial temperature is set and the temperature keeps equilibrium state at every moment. The impact of initial temperature condition in numerical model is decreasing with the increasing of the operational time as shown in Figure 2.
 
 {{< img src="T_out_comparison.png" width="120">}}