"$OUTPUT_FILE"
+$(
+ 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
index 1db94daac1f..ed4c81d2650 100644
--- 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).
+$$
## Input files
diff --git a/web/content/docs/benchmarks/heat-transport-bhe/pipe_flow_EBHE/index.md b/web/content/docs/benchmarks/heat-transport-bhe/pipe_flow_EBHE/index.md
index 6bb1a369d8a..730bdca2367 100644
--- a/web/content/docs/benchmarks/heat-transport-bhe/pipe_flow_EBHE/index.md
+++ b/web/content/docs/benchmarks/heat-transport-bhe/pipe_flow_EBHE/index.md
@@ -25,60 +25,73 @@ Figure 1: Single pipe flow model
In Ramey's analytical solution (Ramey et al. (1962)), the outlet temperature of the pipe inside the wellbore can be calculated by,
-\begin{equation}
+$$
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}
+$$
with dimensionless time $t_D = \frac{\lambda_{s}t}{(\rho_{s}c_{p,s}r_b)}$, the time function $f(t)$ can be calculated by,
-\begin{align}
- &f(t) = [0.4063+0.5\ln(t_D)][1+\frac{0.6}{t_D}], & t_D > 1.5
- \\
- &f(t) = 1.1281\sqrt{t_D}(1-0.3\sqrt{t_D}), & t_D \leqslant 1.5
-\end{align}
+
-\noindent and the overall heat transfer coefficient $U$ is written as follows,
+$$
+ f(t) = [0.4063+0.5\ln(t_D)][1+\frac{0.6}{t_D}], t_D > 1.5
+$$
-\begin{equation}
+
+
+$$
+ 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">}}
diff --git a/web/content/docs/benchmarks/heatconduction/heatconduction-soil-freezing/index.md b/web/content/docs/benchmarks/heatconduction/heatconduction-soil-freezing/index.md
index 7e0e1616c4f..e53f1aafbe1 100644
--- a/web/content/docs/benchmarks/heatconduction/heatconduction-soil-freezing/index.md
+++ b/web/content/docs/benchmarks/heatconduction/heatconduction-soil-freezing/index.md
@@ -21,17 +21,25 @@ Simulations are performed using both our OpenGeoSys platform and the [FreeFem++]
The detailed IBVP problem description for the T+freezing equation, geometric setup, material and model parameters used in the implementation can be found in this document [this PDF document](Heat_conduction_phase_change_(soil_freezing_around_BHE).pdf). The figures below are taken from this documentation and serve for illustrative purposes to give a hint about the modeled process and simulations outcome.
1. We assume the problem to be 3d-axisymmetric and hence opt for reducing it to 2-dimensional setting, as depicted in the figure below. A quarter of a cylindrical soil specimen around a BHE (a quarter of a 3-dimensional domain $\Omega$) and reduction to 2d computational domain $S$:
+
{{< img src="Soil_block.png" >}}
+
Note that $(r,z)\in S$ are denoted as $(x,y)$ which are assumed to be unrelated to the coordinate notations in the original 3d formulation.
2. The initial condition for $T$ in $S$ is assumed to be a positive function which decays linearly from surface to bottom. For modeling the (time-dependent) boundary conditions on $\Gamma_D$ of $S$, it is assumed that within the first $\widehat{t}$ hours, the temperature on $\Gamma_D$ drops continuously from the initial state to the values prescribed by some continuous piecewise linear function of $y$ and such that at the last depth segment it becomes negative. (The latter mimics the impact of the BHE refrigerant with sub-zero temperature.) The figure sketches the situation:
+
{{< img src="T1_soil_block.png" >}}
+
Temperature is given in degrees Celsius. For $t>\widehat{t}$, the prescribed temperature on $\Gamma_D$ and, thus, the heat conduction in the modelled case is triggered by a significant difference between the temperature on $\Gamma_D$ and the initial one within $S$.
3. The results of modelling are depicted in the following two figures, where we plot the temperature distribution in the soil block after 720 hours (30 days) of cooling, and also compare the outcomes of the two corresponding packages:
-{{< img src="T-distribution_(OGS_vs_FF++_2d).png" >}}
-{{< img src="T-distribution_(OGS_vs_FF++_3d).png" >}}
+
+{{< img src="T-distribution_(OGS_vs_FF++*2d).png" >}}
+{{< img src="T-distribution*(OGS_vs_FF++*3d).png" >}}
+
Temperature is given in kelvins. The color legend of $T$ in the corresponding ParaView plots is tuned such that the amount of ice formed around BHEs can be identified. As expected, ice formation occurs in the vicinity of $\Gamma_D$, more specifically, near the segment of $\Gamma_D$ in which the negative temperature has been prescribed. In the rest of the domain, temperature distribution remains almost identical to the initial state, as could also be expected.
4. Finally, the corresponding results from the previous figure are plotted over the three different directed lines within the domain $S$:
-{{< img src="T-over_lines_(OGS_vs_FF++).png" >}}
+
+{{< img src="T-over_lines*(OGS_vs_FF++).png" >}}
+
Here, origin of the horizontal axis on the right plot corresponds to line's origin. For the selected lines, the compared data seems identical point-wise, thus supporting the quantitative similarity of the OGS and FF++ results observed earlier.
### *Remark*
diff --git a/web/content/docs/benchmarks/hydro-component/contracer/index.md b/web/content/docs/benchmarks/hydro-component/contracer/index.md
index f452b05b818..6c175213010 100644
--- a/web/content/docs/benchmarks/hydro-component/contracer/index.md
+++ b/web/content/docs/benchmarks/hydro-component/contracer/index.md
@@ -93,9 +93,9 @@ Both models (1D and 2D) fit the experimental tracer breakthrough curves quite we
The deviance at the peak and tail can be related to the fact that the simulations only consider conservative equilibrium transport (processes that may have occurred in the experimental system such as tracer sorption, non--equilibrium flow and evapotranspiration were not considered in the model).
The differences between the OGS-6 and OGS-5 simulation were very low (RMSQE$=$1.37e-07).
-
+
-
+
## References
diff --git a/web/content/docs/benchmarks/hydro-component/theis/HC_Theis/index.md b/web/content/docs/benchmarks/hydro-component/theis/HC_Theis/index.md
index bae09404234..9d2005053b6 100644
--- a/web/content/docs/benchmarks/hydro-component/theis/HC_Theis/index.md
+++ b/web/content/docs/benchmarks/hydro-component/theis/HC_Theis/index.md
@@ -30,7 +30,7 @@ The setup comprises a 1/8th slice of a full circle (see figure 1).
The outer boundary condition is set as Dirichlet with a hydrostatic pressure along the shell surface of the slice equivalent to a head of $h = 0 m$ (i.e. water level equals top of domain). For mass transport, a Dirichlet boundary conditions with concentration $c = 0$ is set at the outer shell. The inner boundary condition is equivalent to the eighth of a total abstraction rate of $Q_t = 15 m^3/d$ for a full cylinder. *NB: In the `ComponentTransport` process, the Neumann BC is given as mass flux and has to be calculated per area, such that the value for the project file is $Q = Q_t / 8 / A \cdot \rho_0 = 2.83542E-03 m^3/s/m^2 \cdot kg/m^3$ (units equal $\frac{kg}{s m^2}$) with fluid reference density $\rho_0 = 1000 kg/m^3$ and abstraction area $A = 7.65 m^2$.*
-The homogeneous, isotropic domain is defined for the radius $1 < r < 100 m$ and a thickness $b = 10 m$. Saturated intrinsic permeability is $\kappa = 7.6453E-13 m^2$ yielding a transmissivity of $T = 7.5E-05 m^2/s$; porosity is $\phi = 0.2$; specific storage is $S_s = 1.0E-03$ and defined through compressibility $\gamma = 5.0968E-08 s^2/m/kg$ (input tag fluid_density_pressure_difference_ratio is $\gamma = \frac{1}{\rho_0} \frac{\partial \rho}{\partial p}$, which can be used to incorporate $S_s$ with $\gamma = \frac{S_s}{b \phi g \rho_0}$ with gravitational acceleration $g = 9.81 m^2/s$).
+The homogeneous, isotropic domain is defined for the radius $1 < r < 100 m$ and a thickness $b = 10 m$. Saturated intrinsic permeability is $\kappa = 7.6453E-13 m^2$ yielding a transmissivity of $T = 7.5E-05 m^2/s$; porosity is $\phi = 0.2$; specific storage is $S_s = 1.0E-03$ and defined through compressibility $\gamma = 5.0968E-08 s^2/m/kg$ (input tag `fluid_density_pressure_difference_ratio` is $\gamma = \frac{1}{\rho_0} \frac{\partial \rho}{\partial p}$, which can be used to incorporate $S_s$ with $\gamma = \frac{S_s}{b \phi g \rho_0}$ with gravitational acceleration $g = 9.81 m^2/s$).
Mass transport properties are irrelevant as no transport processes are calculated.
diff --git a/web/content/docs/benchmarks/hydro-thermal/constant-viscosity/index.md b/web/content/docs/benchmarks/hydro-thermal/constant-viscosity/index.md
index 6652093921c..3d87579bf75 100644
--- a/web/content/docs/benchmarks/hydro-thermal/constant-viscosity/index.md
+++ b/web/content/docs/benchmarks/hydro-thermal/constant-viscosity/index.md
@@ -17,7 +17,7 @@ See [this PDF](HT-Process.pdf).
This is a 2d benchmark of large-scale thermal convection that tests the temperature dependent fluid density in the hydro-thermal process monolithic approach implementation. It is defined on the domain $\Omega = [0,5500]^2.$
-- The initial conditions for the pressure is a gradient starting from zero at the top surface to a pressure of circa 54 mega pascal at the bottom given in the data array 'initial_pressure' in the VTU file. The initial temperature is also almost a gradient from top (293 K) to bottom (443 K) of the domain, except there is a small perturbation given by adding $\sin \left( \pi \frac{y}{5500}\right) \cdot \cos \left( \pi \frac{x}{5500}\right).$ See the following images.
+- The initial conditions for the pressure is a gradient starting from zero at the top surface to a pressure of circa 54 mega pascal at the bottom given in the data array `initial_pressure` in the VTU file. The initial temperature is also almost a gradient from top (293 K) to bottom (443 K) of the domain, except there is a small perturbation given by adding $\sin \left( \pi \frac{y}{5500}\right) \cdot \cos \left( \pi \frac{x}{5500}\right).$ See the following images.
TODO 3 images
@@ -25,6 +25,6 @@ TODO 3 images
- The further parameter specification can be found in the project file linked at the top of this page.
- The steady state temperature is shown in the following on the right figure. The left figure shows the resulting temperature minus the initial gradient. The resulting temperatures are in good accordance with the FEFLOW results and with results from the OGS version < 6.
-## Comparison with FEFlow solution
+## Comparison with FEFLOW solution
{{< img src="compare.png" >}}
diff --git a/web/content/docs/benchmarks/hydro-thermal/decovalex-TH/index.md b/web/content/docs/benchmarks/hydro-thermal/decovalex-TH/index.md
index e2215e0993a..ff8bddbe999 100644
--- a/web/content/docs/benchmarks/hydro-thermal/decovalex-TH/index.md
+++ b/web/content/docs/benchmarks/hydro-thermal/decovalex-TH/index.md
@@ -21,27 +21,27 @@ The TASK D_THM1 of the DECOVALEX-THMC project studies the coupled thermal hydrau
about the FEBEX type repository \cite BirEtAl:2008. In this example,
TASK D_THM1 is simplified in order to test the staggered scheme for TH process
in OGS. The simplifications are
-
-resizing the domain to an area that can represent the near field of an
- installed nuclear water canister,
assuming the bentonite is fully saturated from the beginning,
ignoring the mechanical process.
-With such simplifications, the geometry of the present example is illustrated
- in the following figure:
+
+1. resizing the domain to an area that can represent the near field of an
+ installed nuclear water canister,
+2. assuming the bentonite is fully saturated from the beginning,
+3. ignoring the mechanical process.
+
+With such simplifications, the geometry of the present example is illustrated
+in the following figure:
+
{{< img src="decovalex_TH_domain.png" >}}
-In the above figure, the domain in the annulus sector represents the sealing
+
+In the above figure, the domain in the annulus sector represents the sealing
material, bentonite. A heat power, which is generated by the nuclear waste with
one million year variation, is applied onto the inner arc of the annulus
sector. On the top boundary, the boundary conditions are
- p = 4.3 ⋅ 106 Pa,
- T = 294 K.
+ $p=4.3 ⋅ 10^6\ \mathrm{Pa}, T=294\ \mathrm{K}$.
While on the bottom boundary, the boundary conditions are set as
- p = 4.7 ⋅ 106 Pa,
- T = 310 K.
+ $p=4.7 ⋅ 10^6\ \mathrm{Pa}, T=319\ \mathrm{K}$.
The initial conditions are given as
- p = 4.7 ⋅ 106 Pa,
- T = 298 K.
+ $p=4.7 ⋅ 10^6\ \mathrm{Pa}, T=298\ \mathrm{K}$.
+
The material properties are shown in the following table:
Material properties
@@ -118,9 +118,9 @@ The TASK D_THM1 of the DECOVALEX-THMC project studies the coupled thermal hydrau
## Solution
-As the reference results, the temperature and pressure distributions in the
+As the reference results, the temperature and pressure distributions in the
domain at the time of 18 years are shown in the following figure, in which the
- thermal convection effective can be seen clearly.
+ thermal convection effective can be seen clearly.
{{< img src="decovalex_TH_domain_pT.png" >}}
diff --git a/web/content/docs/benchmarks/small-deformations/ModifiedCamClay/index.md b/web/content/docs/benchmarks/small-deformations/ModifiedCamClay/index.md
index 1101656ecc9..c2b939723f1 100644
--- a/web/content/docs/benchmarks/small-deformations/ModifiedCamClay/index.md
+++ b/web/content/docs/benchmarks/small-deformations/ModifiedCamClay/index.md
@@ -17,7 +17,7 @@ Five tests are presented:
{{< data-link >}}
of which the last three have the same test program but use different implementations of the modified Cam clay model.
-The mfront-files can be found at [here](https://gitlab.opengeosys.org/ogs/ogs/-/tree/master/MaterialLib/SolidModels/MFront).
+The MFront-files can be found at [here](https://gitlab.opengeosys.org/ogs/ogs/-/tree/master/MaterialLib/SolidModels/MFront).
## Problem description
diff --git a/web/content/docs/benchmarks/th2m/th2m_strain_dependent_permeability/index.md b/web/content/docs/benchmarks/th2m/th2m_strain_dependent_permeability/index.md
index 208d3122c77..d67964cf319 100644
--- a/web/content/docs/benchmarks/th2m/th2m_strain_dependent_permeability/index.md
+++ b/web/content/docs/benchmarks/th2m/th2m_strain_dependent_permeability/index.md
@@ -12,6 +12,6 @@ draft = true
## Problem description
-Todo
+TODO
## Results and evaluation
diff --git a/web/content/docs/benchmarks/thermal-two-phase-flow/TCE-diffusion/index.md b/web/content/docs/benchmarks/thermal-two-phase-flow/TCE-diffusion/index.md
index f74a3cb3cdd..34b20097eae 100644
--- a/web/content/docs/benchmarks/thermal-two-phase-flow/TCE-diffusion/index.md
+++ b/web/content/docs/benchmarks/thermal-two-phase-flow/TCE-diffusion/index.md
@@ -27,9 +27,11 @@ Table 1: Parameters used in the numerical model.
| van Genuchten parameter | $m_{\mathrm{vG}}$ | 0.8 | - |
Atteia and Höhener [[1]](#1) developed a semianalytical solution for the TCE concentration profile at steady state. In their original solution, the effect of hydrodynamic dispersion is also considered. Here, we briefly derive a simplified semianalytical solution for the case without groundwater flow. By using the classical Millington [[2]](#2) formulation for tortuosity, the diffusive flux in either phase $\alpha$ ($\alpha\in \{a, w\}$) can be written as
-\begin{equation}
+
+$$
J_{\alpha}=-nS_{\alpha}\tau_{\alpha}D_{0\alpha}\frac{dx^c_{\alpha}}{dz}=-n^{4/3}S_{\alpha}^{10/3}D_{0\alpha}\frac{dx^c_{\alpha}}{dz}
-\end{equation}
+$$
+
in which $\tau_{\alpha}$ is the tortuosity of phase $\alpha$ and $x^c_{\alpha}$ is molar fraction of TCE in phase $\alpha$. Assuming equilibrium of contaminant concentrations between the liquid and gas phases, we have
\begin{equation}
\frac{N_wx^c_w}{P_gx^c_a}=H
diff --git a/web/content/docs/benchmarks/thermo-hydro-mechanics/massbalance_with_freezing/index.md b/web/content/docs/benchmarks/thermo-hydro-mechanics/massbalance_with_freezing/index.md
index af74d920c82..dddb8f9331a 100644
--- a/web/content/docs/benchmarks/thermo-hydro-mechanics/massbalance_with_freezing/index.md
+++ b/web/content/docs/benchmarks/thermo-hydro-mechanics/massbalance_with_freezing/index.md
@@ -1,7 +1,7 @@
+++
author = "Tymofiy Gerasimov, Dmitri Naumov"
date = "2023-16-6"
-title = "Fully_saturated_column_deformation_and_freezing"
+title = "Fully saturated column deformation and freezing"
project = ["ThermoHydroMechanics/ColumnDeformationFreezing/TM.prj"]
image = "Column_setup.png"
+++
@@ -44,7 +44,7 @@ To assess and analyse our simulation results, we calculate and record at each
time step the vertical component $F_y$ of reaction force on the top boundary
$\Gamma_\mathrm{top}$, namely,
-\begin{equation}
+$$
\boldsymbol F^n=(F^n_x,F^n_y):=\int_{\Gamma_\mathrm{top}}
\boldsymbol\sigma(\boldsymbol u^n)\cdot\boldsymbol n\\, \mathrm{d}s
\quad\text{for $\boldsymbol\sigma \in
@@ -52,7 +52,7 @@ $\Gamma_\mathrm{top}$, namely,
\boldsymbol\sigma_\mathrm{I},
\boldsymbol\sigma_\mathrm{SI}
\\\}$},
-\end{equation}
+$$
where $\boldsymbol u^n:\Omega\rightarrow\mathbb{R}^2$ is the computed
displacement solution vector, and $\boldsymbol n$ is an outward normal on
diff --git a/web/content/docs/devguide/documentation/jupyter-docs/index.md b/web/content/docs/devguide/documentation/jupyter-docs/index.md
index 82ae9b05266..8deecdb3839 100644
--- a/web/content/docs/devguide/documentation/jupyter-docs/index.md
+++ b/web/content/docs/devguide/documentation/jupyter-docs/index.md
@@ -14,10 +14,10 @@ parent = "development-workflows"
## Create a new notebook
-Create a new notebook file in `Tests/Data` (either as regular `.ipynb`-files or as Markdown-based notebooks via [jupytext](https://jupytext.readthedocs.io/en/latest)). See examples:
+Create a new notebook file in `Tests/Data` (either as regular `.ipynb`-files or as Markdown-based notebooks via [Jupytext](https://jupytext.readthedocs.io/en/latest)). See examples:
- [SimpleMechanics.ipynb](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb) (regular `.ipynb`-notebook)
-- [Linear_Disc_with_hole.md](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md) (jupytext-based notebook in Markdown)
+- [Linear_Disc_with_hole.md](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md) (Jupytext-based notebook in Markdown)
## Add web meta information
@@ -38,7 +38,7 @@ If the notebook result should appear as a page on the web documentation a frontm
-In jupytext-based notebooks you can add the frontmatter within the ``- and ``-markers:
+In Jupytext-based notebooks you can add the frontmatter within the ``- and ``-markers:
```md
@@ -125,9 +125,9 @@ ctest -R nb -j 4 --output-on-failure
## Advanced topics
-### jupytext usage
+### Jupytext usage
-If you use the [execution environment](#execution-environment) [jupytext](https://jupytext.readthedocs.io/en/latest) as already configured and its usage is transparent:
+If you use the [execution environment](#execution-environment) [Jupytext](https://jupytext.readthedocs.io/en/latest) is already configured and its usage is transparent:
- Double-click on a markdown file will open it as a Notebook
- Upon saving or executing a linked `.ipynb`-file is created in the background which stores outputs
@@ -140,8 +140,8 @@ On the web site or MR web previews on pages generated by a notebook there is a n
- Click the button to launch the notebook in BinderHub.
-- The environment running in BinderHub is defined in [bilke/binder-ogs-requirements at GitHub](https://github.com/bilke/binder-ogs-requirements)
-- When clicking the link it launches a Jupyter Lab instance pre-configured with ogs [via wheel](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/requirements-ogs.txt#L2), clones the current ogs repo in it and opens the respective notebook ready to run. Please note that startup times may be several minutes and the computing resources are limited (1 core, 2GB RAM). For improved performance we would need to setup own infrastructure. Also currently only works for serial ogs configs.
+- The environment running in BinderHub is defined in [`bilke/binder-ogs-requirements` at GitHub](https://github.com/bilke/binder-ogs-requirements)
+- When clicking the link it launches a Jupyter Lab instance pre-configured with ogs [via wheel](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/requirements-ogs.txt#L2), clones the current ogs repo in it and opens the respective notebook ready to run. Please note that startup times may be several minutes and the computing resources are limited (1 core, 2GB RAM). For improved performance we would need to setup own infrastructure. Also currently only works for serial ogs configurations.
### PyVista notebooks on headless Linux systems
diff --git a/web/content/docs/devguide/documentation/todo/index.md b/web/content/docs/devguide/documentation/todo/index.md
index 38d5ab1ba51..a03619af523 100644
--- a/web/content/docs/devguide/documentation/todo/index.md
+++ b/web/content/docs/devguide/documentation/todo/index.md
@@ -8,12 +8,13 @@ weight = 1027
This list was obtained using grep and added here to provide an overview of what sections are missing the documentation. In the future it should be generated automatically.
-It can be obtained by running script ```todo-check.sh``` from ```/web/content/docs/userguide``` folder.
+It can be obtained by running script `todo-check.sh` from `web/content/docs/userguide` folder.
-## TODOs in userguide/basics
+## TODOs in `userguide/basics`
-## TODOs in userguide/blocks
-```
+## TODOs in `userguide/blocks`
+
+```bash
blocks/curves.md-19-
blocks/curves.md-20-
blocks/curves.md:21:TODO: Add general description
@@ -95,8 +96,9 @@ blocks/processes.md-158-
blocks/processes.md:159:The global non-linear equation system can be solved either with Picard fix-point iterations or a Newton scheme. (TODO: Reference NLS scheme)
```
-## TODOs in userguide/features
-```
+## TODOs in `userguide/features`
+
+```bash
features/python_bc.md-31-## Using python boundary condition in project file
features/python_bc.md-32-
features/python_bc.md:33:TODO: add description of how to call python bc from the boundary condition tag
@@ -122,5 +124,4 @@ features/mfront.md-109-
features/mfront.md:110:TODO: add content
```
-## TODOs in userguide/troubleshooting
-
+## TODOs in `userguide/troubleshooting`
diff --git a/web/content/docs/devguide/documentation/web-docs/index.md b/web/content/docs/devguide/documentation/web-docs/index.md
index 1cf45a36a05..8f26d079b7d 100644
--- a/web/content/docs/devguide/documentation/web-docs/index.md
+++ b/web/content/docs/devguide/documentation/web-docs/index.md
@@ -88,7 +88,7 @@ We use [Markdown](https://commonmark.org/help/) for the actual content. Hugo use
Use regular Markdown syntax:
-```md
+```markdown
```
@@ -96,7 +96,7 @@ The path to the image is the relative path to the current [page bundle](https://
You can add size attributes to the filename with a `#`-character:
-```md
+```markdown
```
diff --git a/web/content/docs/devguide/getting-started/build-configuration/index.md b/web/content/docs/devguide/getting-started/build-configuration/index.md
index 57fccab4fb3..f0dda1acd38 100644
--- a/web/content/docs/devguide/getting-started/build-configuration/index.md
+++ b/web/content/docs/devguide/getting-started/build-configuration/index.md
@@ -146,7 +146,7 @@ CC=mpicc CXX=mpic++ cmake ../ogs -G Ninja -DCMAKE_BUILD_TYPE=Release -DOGS_USE_P
-CMake comes with a graphical tool called **cmake-gui**. You can find it in the **Windows Start Menu**. First you need to set the source and build directory. Then click **Configure**. Now choose the generator to be used (e.g. **Visual Studio {{< dataFile "versions.minimum_version.msvc.number" >}} {{< dataFile "versions.minimum_version.msvc.year" >}}** for Visual Studio {{< dataFile "versions.minimum_version.msvc.year" >}}). Now choose your desired configuration options by toggling the corresponding checkboxes. Click **Configure** again. Click **Configure** often enough until the **Generate**-button becomes visible. Pressing **Generate** will finally generate the project files inside the chosen build directory.
+CMake comes with a graphical tool called `cmake-gui`. You can find it in the **Windows Start Menu**. First you need to set the source and build directory. Then click **Configure**. Now choose the generator to be used (e.g. **Visual Studio {{< dataFile "versions.minimum_version.msvc.number" >}} {{< dataFile "versions.minimum_version.msvc.year" >}}** for Visual Studio {{< dataFile "versions.minimum_version.msvc.year" >}}). Now choose your desired configuration options by toggling the corresponding checkboxes. Click **Configure** again. Click **Configure** often enough until the **Generate**-button becomes visible. Pressing **Generate** will finally generate the project files inside the chosen build directory.
diff --git a/web/content/docs/devguide/getting-started/build-configuration_for_MPI_PETSc/configure_for_mpi_and_petsc.md b/web/content/docs/devguide/getting-started/build-configuration_for_MPI_PETSc/configure_for_mpi_and_petsc.md
index 5774336d10b..13a13c06461 100644
--- a/web/content/docs/devguide/getting-started/build-configuration_for_MPI_PETSc/configure_for_mpi_and_petsc.md
+++ b/web/content/docs/devguide/getting-started/build-configuration_for_MPI_PETSc/configure_for_mpi_and_petsc.md
@@ -21,7 +21,7 @@ has many derivatives, e.g intelMPI) has to be installed as prerequisite.
PETSc is not supported on Windows system.
As an alternative you can follow the instructions in Section [Install PETSc manually](#install-petsc-manually) and run PETSc using Cygwin or use Windows Subsystem For Linux (WSL).
The latter option is recommended - using WSL.
-The manual of setting up OpenGeoSys in WSL can be found in our [Windows Subsystem For Linux]({{[}}) guide.
+The manual of setting up OpenGeoSys in WSL can be found in our [Windows Subsystem For Linux]({{< ref "wsl" >}}) guide.
After setting up WSL, please follow the Linux tab in this guide.
@@ -30,7 +30,7 @@ After setting up WSL, please follow the Linux tab in this guide.
## Set up prerequisites
-Before continuing with this guide, please follow all steps from the "Developer guide" articles: [Set Up Prerequisites]({{][}}) and [Get the source code]({{][}}).
+Before continuing with this guide, please follow all steps from the "Developer guide" articles: [Set Up Prerequisites]({{< ref "prerequisites" >}}) and [Get the source code]({{< ref "get-the-source-code" >}}).
### Install MPI
@@ -88,7 +88,7 @@ cmake --build --preset release-petsc
```
The ```release-petsc``` preset is based on the ```release``` preset.
-It can be customized by passing additional variable with ```-D``` flags to cmake command.
+It can be customized by passing additional variable with ```-D``` flags to `cmake` command.
If you want to install PETSc yourself, please see Section [Install PETSc](#install-petsc-manually).
@@ -134,7 +134,7 @@ Please note, that the PETSc package is usually build in release mode independent
]
-PESTSc is recommended to use on Linux.
+PETSc is recommended to use on Linux.
On Windows, it only runs on UNIX emulator Cygwin.
A detailed description about how to use PETSc on Windows is available on this PETSc site:
.
diff --git a/web/content/docs/devguide/getting-started/build/index.md b/web/content/docs/devguide/getting-started/build/index.md
index eef1ee3a256..efd53c2c2a5 100644
--- a/web/content/docs/devguide/getting-started/build/index.md
+++ b/web/content/docs/devguide/getting-started/build/index.md
@@ -38,7 +38,7 @@ cd build-directory
cmake --build . --config Release
```
-Please that with Visual Studio you have to provide the `--config`-paramter as Visual Studio is a [multi-configuration generator](https://cmake.org/cmake/help/latest/prop_gbl/GENERATOR_IS_MULTI_CONFIG.html) in CMake.
+Please that with Visual Studio you have to provide the `--config`-parameter as Visual Studio is a [multi-configuration generator](https://cmake.org/cmake/help/latest/prop_gbl/GENERATOR_IS_MULTI_CONFIG.html) in CMake.
If you build with the help of a [CMake preset]({{< ref "build-configuration#available-cmake-presets" >}}) then you can omit the `--config`-parameter, e.g.:
diff --git a/web/content/docs/devguide/packages/python-env/index.md b/web/content/docs/devguide/packages/python-env/index.md
index 887d241a9f0..e703e3c6d19 100644
--- a/web/content/docs/devguide/packages/python-env/index.md
+++ b/web/content/docs/devguide/packages/python-env/index.md
@@ -31,7 +31,7 @@ To manually add Python packages run the following inside your build-directory:
.venv/bin/pip install python-package-name
```
-To activate the environment run `source .venv/bin/activate` inside your build directory. If you have the [direnv](https://direnv.net)-tool installed and setup the virtual environment will be activated automatically upon changing into the build directory.
+To activate the environment run `source .venv/bin/activate` inside your build directory. If you have the [`direnv`](https://direnv.net)-tool installed and setup the virtual environment will be activated automatically upon changing into the build directory.
### Pip & Benchmarks
diff --git a/web/content/docs/devguide/testing/gitlab-ci/index.md b/web/content/docs/devguide/testing/gitlab-ci/index.md
index e7fce01fba5..3c53257279a 100644
--- a/web/content/docs/devguide/testing/gitlab-ci/index.md
+++ b/web/content/docs/devguide/testing/gitlab-ci/index.md
@@ -68,7 +68,7 @@ You can change the pipeline by editing the `.gitlab-ci.yml` and `scripts/ci/jobs
These variables in `.gitlab-ci.yml` modify the pipeline:
- `BUILD_TESTS`: Set this to `false` to disable unit tests.
-- `BUILD_CTEST`: Set this to `false` to disable ctest (benchmark) tests.
+- `BUILD_CTEST`: Set this to `false` to disable CTest (benchmark) tests.
- `CTEST_ARGS`: Supply additional arguments to the `ctest`-command to select which benchmarks are run, e.g.:
- `-R nb` would select all notebook-based tests and would disable all other benchmarks
- `-LE large` would exclude all tests with label `large`
diff --git a/web/content/docs/processes/component-transport/hydro-component/index.md b/web/content/docs/processes/component-transport/hydro-component/index.md
index 6ef881c4e6c..8923bd97715 100644
--- a/web/content/docs/processes/component-transport/hydro-component/index.md
+++ b/web/content/docs/processes/component-transport/hydro-component/index.md
@@ -39,9 +39,11 @@ $$
\end{equation}
$$
with the concentration $c_{\alpha}$ of the chemical component as the primary variable. $D$ [m$^2$/s] denotes the hydrodynamic dispersion tensor with the following relation
-\begin{equation}
+
+$$
D = (\phi D_{p} + \beta_T \lVert \textbf{q} \rVert) \textbf{I} + （ \beta_L - \beta_T ） \frac{\textbf{q} \textbf{q}^{T}}{\lVert \textbf{q} \rVert}
-\end{equation}
+$$
+
implemented, where $D_p$ [m$^2$/s] is the pore diffusion coefficient, $\beta_L$ and $\beta_T$ [m] are the longitudinal and transversal dispersion coefficients. $R$ [-] is the retardation factor defined as
$$
R = 1 + \rho_{b} K_{D} / \phi
diff --git a/web/content/docs/processes/heat-transport/HEAT_TRANSPORT_BHE/index.md b/web/content/docs/processes/heat-transport/HEAT_TRANSPORT_BHE/index.md
index 2b0da050510..c09af614b4f 100644
--- a/web/content/docs/processes/heat-transport/HEAT_TRANSPORT_BHE/index.md
+++ b/web/content/docs/processes/heat-transport/HEAT_TRANSPORT_BHE/index.md
@@ -37,10 +37,10 @@ Here, $\Lambda_s$ denotes the tensor of thermal hydrodynamic dispersion and $H_s
In the configuration of `HEAT_TRANSPORT_BHE` process, it is generally configured as follows.
-* < name >: should be `HeatTransportBHE`.
-* < type >: should be `HEAT_TRANSPORT_BHE`.
-* < integration_order >: It is the order of the integration method for element-wise integration, normally set to 2.
-* < process_variables >: The primary variables of the `HEAT_TRANSPORT_BHE` process are `temperature_soil` and `temperature_BHE1`. For multiple boreholes, the name `temperature_BHE2`, `temperature_BHE3` etc can be added.
+* `
`: should be `HeatTransportBHE`.
+* ``: should be `HEAT_TRANSPORT_BHE`.
+* ``: It is the order of the integration method for element-wise integration, normally set to 2.
+* ``: The primary variables of the `HEAT_TRANSPORT_BHE` process are `temperature_soil` and `temperature_BHE1`. For multiple boreholes, the name `temperature_BHE2`, `temperature_BHE3` etc can be added.
```xml
HeatTransportBHE
diff --git a/web/content/docs/processes/heat-transport/Heat_Transport_BHE_PipelineNetwork/index.md b/web/content/docs/processes/heat-transport/Heat_Transport_BHE_PipelineNetwork/index.md
index 2547d625465..892c825e854 100644
--- a/web/content/docs/processes/heat-transport/Heat_Transport_BHE_PipelineNetwork/index.md
+++ b/web/content/docs/processes/heat-transport/Heat_Transport_BHE_PipelineNetwork/index.md
@@ -172,7 +172,7 @@ The work flow of the PipeNetwork feature is illustrated in Figure 2. To explicit
### BHE data container
-In order to use the PipeNetwork feature, the pre-built and saved TESPy network model in the above section is required. A CSV file `bhe_network.csv` which containing all the OGS-TESPy transferred BHE's information needs to be created. The PipeNetwork feature will access this CSV file to initialize the exchange data container between OGS and TESPy during the simulation. All BHEs have to be included in this CSV file. Please take notice that all BHE names located in the data_index column have to be identical with the BHE names defined in the corresponding TESPy network model.
+In order to use the PipeNetwork feature, the pre-built and saved TESPy network model in the above section is required. A CSV file `bhe_network.csv` which contains all the OGS-TESPy transferred BHE information needs to be created. The PipeNetwork feature will access this CSV file to initialize the exchange data container between OGS and TESPy during the simulation. All BHEs have to be included in this CSV file. Please take notice that all BHE names located in the `data_index` column have to be identical with the BHE names defined in the corresponding TESPy network model.
```bash
data_index;BHE_id;Tin_val;Tout_val;Tout_node_id;flowrate
diff --git a/web/content/docs/processes/thermal-processes/THM/index.md b/web/content/docs/processes/thermal-processes/THM/index.md
index e5d3e34d144..106395da94d 100644
--- a/web/content/docs/processes/thermal-processes/THM/index.md
+++ b/web/content/docs/processes/thermal-processes/THM/index.md
@@ -59,9 +59,9 @@ THM process has to be declared in project file in the processes block. For examp
Following process variables are available in THM process:
-- temperature
-- pressure
-- displacement
+- `temperature`
+- `pressure`
+- `displacement`
For more details, see [Process variables]({{< ref "process_variables" >}}).
diff --git a/web/content/docs/processes/thermal-processes/TRM/index.md b/web/content/docs/processes/thermal-processes/TRM/index.md
index da4da584cb4..70af681b264 100644
--- a/web/content/docs/processes/thermal-processes/TRM/index.md
+++ b/web/content/docs/processes/thermal-processes/TRM/index.md
@@ -1,7 +1,7 @@
+++
author = "Feliks Kiszkurno, Wenqing Wang"
date = "2023-01-10"
-title = "Thermo Richards Mechanics Process"
+title = "Thermo-Richards-Mechanics Process"
weight = 2
+++
@@ -74,7 +74,7 @@ $$
$$
with $\mathbf{\sigma}$ the effective stress tensor, $b(S)$ the Bishop model, $\mathbf f$ the body force, and $\mathbf I$ the identity.
- The primary unknowns of the momentum balance equation are the displacement $\mathbf u$, which is associated with the stress by the the generalized Hook's law as
+ The primary unknowns of the momentum balance equation are the displacement $\mathbf u$, which is associated with the stress by the generalized Hook's law as
$$
{\dot {\mathbf {\sigma}}} = C {\dot {\mathbf \epsilon}}^e
= C ( {\dot {\mathbf \epsilon}} - {\dot {\mathbf \epsilon}}^T
@@ -124,7 +124,7 @@ Those properties are defined on the phase level for each medium. See [phase prop
| Vapour density | Yes | No | No | No | No | WaterVapourDensity |
| Vapour diffusion | Yes | No | No | No | No | VapourDiffusionFEBEX |
| Thermal expansivity | No | Yes | No | No | Yes | - |
-| Thermo osmosis coefficient | No | Yes | No | No | No | - |
+| Thermo-osmosis coefficient | No | Yes | No | No | No | - |
### Medium properties
@@ -158,9 +158,9 @@ TRM process has to be declared in the project file in the processes block. For e
Following process variables are available in TRM process:
-- temperature
-- pressure
-- displacement
+- `temperature`
+- `pressure`
+- `displacement`
For more details, see [Process variables]({{< ref "process_variables" >}}).
diff --git a/web/content/docs/tools/fileio/GocadTSurfaceReader/index.md b/web/content/docs/tools/fileio/GocadTSurfaceReader/index.md
index d9541bab6d9..e5c79778bb3 100644
--- a/web/content/docs/tools/fileio/GocadTSurfaceReader/index.md
+++ b/web/content/docs/tools/fileio/GocadTSurfaceReader/index.md
@@ -16,7 +16,7 @@ At the moment, this utility can read:
Expected file extensions for these data types include *.vs,*.pl, *.ts, and*.mx (the last one for **m**i**x**ed data).
-Another data type, SGRID (Structured Grid, usually saved to `.sg` files) can be converted via the [GoCadSGridReader](../../meshing/gocadsgridreader).
+Another data type, SGrid (Structured Grid, usually saved to `.sg` files) can be converted via the [GoCadSGridReader](../../meshing/gocadsgridreader).
Parsers for additional GOCAD-datasets may be added in the future.
diff --git a/web/content/docs/tools/fileio/OGS2VTK/index.md b/web/content/docs/tools/fileio/OGS2VTK/index.md
index f80574ec006..0bb3517450f 100644
--- a/web/content/docs/tools/fileio/OGS2VTK/index.md
+++ b/web/content/docs/tools/fileio/OGS2VTK/index.md
@@ -5,14 +5,17 @@ author = "Julian Heinze"
+++
## Description
-OGS2VTK is a tool to convert OGS-mesh-files to VTK-files.
+
+OGS2VTK is a tool to convert OGS-mesh-files to VTK-files.
It can be applied to format OGS-5 legacy mesh files or visualize them in ParaView.
+
## Usage
+
```bash
-USAGE:
+USAGE:
OGS2VTK [--ascii_output] -o -i [--] [--version] [-h]
-Where:
+Where:
--ascii_output
Write VTU output in ASCII format. Due to possible rounding the ascii
@@ -33,8 +36,11 @@ Where:
-h, --help
Displays usage information and exits.
```
-## Example:
-Converting a .msh-file to a .vtu-file.
+
+## Example
+
+Converting a `.msh`-file to a `.vtu`-file.
+
```bash
OGS2VTK -i example.msh -o example.vtu
-```
\ No newline at end of file
+```
diff --git a/web/content/docs/tools/fileio/TIN2VTK/index.md b/web/content/docs/tools/fileio/TIN2VTK/index.md
index 51dc44ef59b..f9bc6c50a1f 100644
--- a/web/content/docs/tools/fileio/TIN2VTK/index.md
+++ b/web/content/docs/tools/fileio/TIN2VTK/index.md
@@ -5,17 +5,19 @@ author = "Julian Heinze"
+++
## Description
+
This tool converts datasets in TIN-format, usually used in geographic information systems (GIS), into VTK-format.
The TIN-format stores triangular irregular networks which can be considered a subclass of triangulated 2D meshes.
-VTK stores such irregular networks as unstructured grids in *.vtu-files.
+VTK stores such irregular networks as unstructured grids in `*.vtu`-files.
## Usage
+
```bash
-USAGE:
+USAGE:
TIN2VTK -o -i [--] [--version] [-h]
-Where:
+Where:
-o , --output-vtu-file
(required) the name of the file the mesh will be written to
@@ -32,8 +34,8 @@ Where:
Displays usage information and exits.
```
-## Example:
+## Example
```bash
TIN2VTK -i input.tin -o output.vtu
-```
\ No newline at end of file
+```
diff --git a/web/content/docs/tools/fileio/VTK2TIN/index.md b/web/content/docs/tools/fileio/VTK2TIN/index.md
index 8f3c657f0bc..e12739c10f3 100644
--- a/web/content/docs/tools/fileio/VTK2TIN/index.md
+++ b/web/content/docs/tools/fileio/VTK2TIN/index.md
@@ -5,16 +5,19 @@ author = "Julian Heinze"
+++
## Description
-This tool converts VTK unstructured grids (*.vtu) into TIN-format usable in geographic information systems (GIS).
-The TIN-format stores triangular irregular networks which can be considered a subclass of triangulated 2D meshes.
-The vtu-format can store a large variety of unstructured mesh types, but only 2D triangle meshes can be converted using this tool.
+
+This tool converts VTK unstructured grids (`*.vtu`) into TIN-format usable in geographic information systems (GIS).
+The TIN-format stores triangular irregular networks which can be considered a subclass of triangulated 2D meshes.
+The VTU-format can store a large variety of unstructured mesh types, but only 2D triangle meshes can be converted using this tool.
+
## Usage
+
```bash
-USAGE:
+USAGE:
TIN2VTK -o -i [--] [--version] [-h]
-Where:
+Where:
-o , --output-vtu-file
(required) the name of the file the mesh will be written to
@@ -31,8 +34,8 @@ Where:
Displays usage information and exits.
```
-## Example:
+## Example
```bash
VTK2TIN -i input.vtu -o output.tin
-```
\ No newline at end of file
+```
diff --git a/web/content/docs/tools/geometries/generateGeometry/index.md b/web/content/docs/tools/geometries/generateGeometry/index.md
index 7a509c9407f..63e4a2102f3 100644
--- a/web/content/docs/tools/geometries/generateGeometry/index.md
+++ b/web/content/docs/tools/geometries/generateGeometry/index.md
@@ -6,28 +6,31 @@ weight = 1
+++
## Description
-This tool is used to generate either a quad/rectangle or a line.
+
+This tool is used to generate either a quad/rectangle or a line.
For this purpose, two points are used to define the geometry.
-To create a quad, the defining points need to be in a plane parallel to the xy-, xz- or yz-plane.
-To create a line, they must define a line parallel to the standard basis vectors of 3D space.
+To create a quad, the defining points need to be in a plane parallel to the XY-, YZ- or YZ-plane.
+To create a line, they must define a line parallel to the standard basis vectors of 3D space.
Quads and lines then can be combined to create more complex geometries.
-This tool is mainly used to create simple geometries for benchmarking or testing purposes.
+This tool is mainly used to create simple geometries for benchmarking or testing purposes.
+
## Usage
+
```bash
-USAGE:
- generateGeometry -o
diff --git a/web/content/docs/userguide/features/python_bc.md b/web/content/docs/userguide/features/python_bc.md
index 44335f73dec..86b1ff598df 100644
--- a/web/content/docs/userguide/features/python_bc.md
+++ b/web/content/docs/userguide/features/python_bc.md
@@ -73,10 +73,10 @@ OpenGeoSys will obtain values for a Dirichlet boundary condition by calling the
The following variables are always passed as an input to the Dirichlet boundary condition method (in brackets the default
variable name used in examples) is given:
-- time (t),
-- spatial coordinates (coords),
-- node id (node_id),
-- primary variables (primary_vars).
+- time (`t`),
+- spatial coordinates (`coords`),
+- node id (`node_id`),
+- primary variables (`primary_vars`).
#### Output
@@ -91,15 +91,15 @@ The order in which those variables are provided is important.
### Neumann boundary condition
-OpenGeoSys will obtain values for a Neumann boundary condition by calling the method "getFlux".
+OpenGeoSys will obtain values for a Neumann boundary condition by calling the method `getFlux`.
#### Input
The following variables are always passed as an input to the Dirichlet boundary condition method (in brackets the default variable name used in examples is given):
-- time (t),
-- spatial coordinates (coords),
-- primary variables (primary_vars).
+- time (`t`),
+- spatial coordinates (`coords`),
+- primary variables (`primary_vars`).
The order in which those variables are provided is important.
diff --git a/web/content/docs/userguide/troubleshooting/faq.md b/web/content/docs/userguide/troubleshooting/faq.md
index b8d81aab9f3..1a170552c1b 100644
--- a/web/content/docs/userguide/troubleshooting/faq.md
+++ b/web/content/docs/userguide/troubleshooting/faq.md
@@ -5,7 +5,7 @@ author = "Lars Bilke and Feliks Kiszkurno"
weight = 1
+++
-## "XSDError: Loaded schema file is invalid" error encountered when running DataExplorer
+## `XSDError: Loaded schema file is invalid` error encountered when running DataExplorer
You may encounter the following error (or similar) on opening `.gml`, `.cnd`, `std` or `.prj` files in the Data Explorer or file
conversion tools (e.g., `OGSFileConverter`):
diff --git a/web/content/docs/userguide/troubleshooting/general/index.md b/web/content/docs/userguide/troubleshooting/general/index.md
index 58ff5fe1a8f..3bb491d71bf 100644
--- a/web/content/docs/userguide/troubleshooting/general/index.md
+++ b/web/content/docs/userguide/troubleshooting/general/index.md
@@ -10,7 +10,7 @@ toc = true
## Data Explorer
-### XSDError: Loaded schema file is invalid
+### `XSDError`: Loaded schema file is invalid
You may encountering the following error (or similar) on opening `.gml`, `.cnd`, `std` or `.prj` files in the Data Explorer or
file conversion tools (e.g. `OGSFileConverter`):