Merge branch 'develop' of https://github.com/feelpp/book.feelpp.org i…

…nto develop

.github/workflows/main.yml

@@ -16,7 +16,10 @@ jobs:
 #        python-version: '3.10'
 #        cache: 'pip' # caching pip dependencies
     - name: Python install 
-      run: pip install -r requirements.txt        
+      run: |
+        python -m venv --system-site-packages .venv
+        source .venv/bin/activate
+        pip install -r requirements.txt        
     - name: Npm Install 
       run: |
         npm i 
@@ -27,7 +30,9 @@ jobs:
         asciidoctor -v
 
     - name: Build
-      run: npm run antora
+      run: |
+        source .venv/bin/activate
+        npm run antora
       env:
         FEELPP_GITHUB_TOKEN: ${{ secrets.DOCS_GITHUB_KEY }}
         GITHUB_OAUTH: ${{ secrets.DOCS_GITHUB_KEY }}

.gitignore

@@ -38,3 +38,6 @@ jupyter/
 /**/node_modules/
 /**/build/
 /**/feelppdb/
+/**/toto/
+/**/*DS_Store
+

docs/mor/modules/ROOT/nav.adoc

@@ -1,10 +0,0 @@
-* xref:toolboxmor.adoc[ToolboxMor]
-** xref:toolboxmor.adoc#_creating_a_model_from_scratch[Creating a model from scratch]
-** xref:toolboxmor.adoc#_creating_a_model_from_a_toolbox[Creating a model from a toolbox]
-** xref:toolboxmor.adoc#_configuration[Configuration]
-* xref:pbdw.adoc[PBDW]
-** xref:pbdw.adoc#_sensors[Sensors]
-** xref:pbdw.adoc#_using_pbdw[Using PBDW]
-* xref:index.adoc#_cases[Cases]
-** xref:opusheat:index.adoc[OpusHeat]
-** xref:thermalfin:index.adoc[ThermalFin]

docs/mor/modules/ROOT/pages/index.adoc

@@ -1,15 +1,6 @@
 = Model Order Reduction
+:page-layout: case-study
+:page-tags: toolbox
 
 Welcome to the documentation of the Feel++ Model Order Reduction.
 
-== Introduction
-
-Feel++ provides a framework for model order reduction. +
-One easy way to use it, is to use the xref:toolboxmor.adoc[ToolboxMor] class.
-
-The Parametrized Background Data Weak (xref:pbdw.adoc[PBDW]) method has also been implemented in Feel++.
-
-== Cases
-
-- xref:opusheat:index.adoc[OpusHeat]
-- xref:thermalfin:index.adoc[ThermalFin]

docs/mor/modules/opusheat/pages/index.adoc → docs/mor/modules/ROOT/pages/opusheat/index.adoc

@@ -1,4 +1,8 @@
 = Opus Heat
+:page-tags: case
+:page-illustration: opusheat/eads_geometry.png
+:description: We consider a reduced 2D model of the surroundings of an electronic component submitted to a cooling air flow.
+
 
 This test case has been proposed by mailto:[email protected][Annabelle Le-Hyaric] and
 mailto:[email protected][Michel Fouquembergh] formerly at AIRBUS.
@@ -28,7 +32,7 @@ stem:[k_1] and stem:[k_2] are parameters of the model.
 
 ICs dissipate heat, so the volumic heat dissipated stem:[Q_1] and stem:[Q_2] are also parameters of the model, while stem:[Q_3=Q_4=0].
 
-image::eads_geometry.png[]
+image::opusheat/eads_geometry.png[]
 
 One should notice that the convection term in heat transfer equation
 may lead to spatial oscillations which can be overcome by

docs/mor/modules/ROOT/pages/pbdw.adoc

@@ -1,4 +1,7 @@
 = Parametrized Background Data Weak
+:page-tags: manual
+:description: PBDW manual
+:page-illustration: pass:[toolboxes::manual.svg]
 
 == Sensors
 

docs/mor/modules/ROOT/pages/thermalbuilding/index.adoc

@@ -0,0 +1,135 @@
+= Thermal simulation of 3D building
+:stem: latexmath
+:page-tags: case
+:page-illustration: thermalbuilding/3d_building.png
+:description: We create a reduced order model for the thermal simulation of a 3D building using the stationary heat equation.
+:uri-data: https://github.com/feelpp/feelpp/blob/develop/mor/examples/thermalbuilding/
+
+== Description
+
+Based on the solution of the stationary heat equation, we create a reduced order model for the simulation of heat exchanges in a 3D building. 
+
+The building is composed of a corridor and 5 rooms, each of which contains a heating unit. Internal walls and doors are modelled as having finite thickness, while external walls properties (thickness and insulation) are encoded in the boundary conditions of the problem.
+
+// Image
+
+=== Mathematical model
+
+Let stem:[\Omega \subset \mathbb{R}^3] be the region occupied by the building, and denote stem:[\Omega_i], stem:[i=0,1,2] its subregions occupied by the air, the internal walls and the internal doors, such that stem:[\Omega = \cup_{i=0}^2 \Omega_i]. Let stem:[k_i] be the thermal conductivities associated with the subregions.
+
+The external boundary of the domain stem:[\partial \Omega] is decomposed into two parts: stem:[\partial \Omega_{ext}], which corresponds to external walls, and stem:[\partial \Omega_D] which corresponds to the front door. We denote by stem:[\Gamma_i] the boundary of the stem:[i-]th heating unit, stem:[i=0,...,4]. The problem writes as
+
+[stem]
+++++
+\begin{equation}
+\begin{aligned}
+- \nabla \cdot (k_i\nabla u) &= 0, \quad &\text{on }\Omega_i \\
+u &= \mu_i \quad &\text{on }\Gamma_i, i=0,...,4, \\
+-  k_0 \nabla u \cdot \vec{n} &= \mu_6 (u - \mu_5), \quad &\text{on }\partial \Omega_{ext},\\
+-  k_0 \nabla u \cdot \vec{n} &= \sigma (u - \mu_5), \quad &\text{on }\partial \Omega_{D}.
+\end{aligned}
+\end{equation}
+++++
+where stem:[\sigma] is the convective heat exchange coefficient associated with the front door.
+
+The parameters stem:[\mu_i] correspond to 
+
+* stem:[\mu_i \in (300,340)], for stem:[i=0,...,4], are the surface temperatures of the heating units (in Kelvin);
+* stem:[\mu_5 \in (270,290)] is the external temperature (in Kelvin);
+* stem:[\mu_6] is a function of the external wall thickness. The wall is composed of two layers: a cinder layer of thickness stem:[l_{cinder} \in (0.1,0.3) m] and an insulation layer of thickness stem:[l_{insulation} \in (0.1,0.2) m], and
+
+[stem]
+++++
+\mu_6 = \frac{1}{0.06 + \frac{0.01}{0.5} + \frac{l_{cinder}}{0.8} + \frac{l_{insulation}}{0.032} + \frac{0.016}{0.313} + 0.14}.
+++++
+
+=== Construction of the affine decomposition
+
+The problem presents an affine dependence on the parameters, hence we can explicity compute the terms of the correspondent affine decomposition
+
+[stem]
+++++
+\sum_{i = 0}^{N_A} \theta^A_i(\mu) A_i(u,v) = \sum_{j = 0}^{N_F} \theta^F_j(\mu) F_j(v),
+++++
+where stem:[N_A = 1] and stem:[N_F = 6].
+
+The first product on the left-hand side is given by stem:[\theta^A_0(\mu) = 1] and 
+
+[stem]
+++++
+\begin{equation}
+\begin{aligned}
+A_0(u,v) &= \sum_{i=0}^{N_m} \int_{\Omega_i} k_i \nabla u \cdot \nabla v + \\
+ & - \int_{\partial \Omega_{ext}} k_0 (\nabla u v + \nabla v u )\cdot \vec{n} +  \\
+ & + \int_{\partial \Omega_{ext}} k_0 \frac{\gamma}{h} u v  +\\
+ & + \int_{\partial \Omega_D} uv, 
+\end{aligned}
+\end{equation}
+++++ 
+
+where stem:[\gamma] is the Nitsche penalty parameter and stem:[h] is the local mesh size.
+
+The second product is given by stem:[\theta^A_1(\mu) = \mu_6] and
+
+[stem]
+++++
+A_1(u,v) = \int_{\partial \Omega_{ext}} u v.
+++++
+
+The terms on the right-hand side are stem:[\theta^F_i(\mu) = \mu_i] for stem:[i=0,...,4], corresponding to the temperatures of the heating units, stem:[\theta^F_5(\mu) = \mu_5\mu_6], corresponding to the temperature on the internal surface of the external walls, and stem:[\theta^F_6(\mu) = \mu_5], corresponding to the external temperature. The corresponding linear forms are 
+
+[stem]
+++++
+\begin{equation}
+\begin{aligned}
+F_i (v) &= k_0 \int_{\Gamma_i} -\nabla v \cdot \vec{n} + \frac{\gamma}{h} v, \quad i = 0,...,4\\
+F_5 (v) &= \int_{\partial \Omega_{ext}} v,\\
+F_6 (v) &= \int_{\partial \Omega_D} \sigma v.
+\end{aligned}
+\end{equation}
+++++
+
+=== Geometry
+
+image::thermalbuilding/heat_3d.png[]
+
+The geometry file can be found in Github link:{uri-data}/thermalbuilding/thermalbuilding.geo[here].
+
+== Output
+
+The output corresponds to the air mean temperature, and it is computed as 
+
+[stem]
+++++
+\begin{equation}
+s(\mu) = \frac{1}{|\Omega_0|} \int_{\Omega_0} u.
+\end{equation}
+++++
+
+== Parameters
+
+The table displays the various fixed and variables parameters of this test-case.
+
+.Table of model order reduction parameters
+[width="100%"]
+|=======================================================================
+| Name         | Description                    | Range                 | Units
+| stem:[\mu_0] | Heater temperature living room | stem:[[300,340]]      | stem:[K]
+| stem:[\mu_1] | Heater temperature kitchen     | stem:[[300,340]]      | stem:[K]
+| stem:[\mu_2] | Heater temperature bedroom 1   | stem:[[300,340]]      | stem:[K]
+| stem:[\mu_3] | Heater temperature bedroom 2   | stem:[[300,340]]      | stem:[K]
+| stem:[\mu_4] | Heater temperature bathroom    | stem:[[300,340]]      | stem:[K]
+| stem:[\mu_5] | External temperature           | stem:[[270,290]]      | stem:[K]
+| stem:[\mu_6] | Exchange coefficient external walls |                  | 
+|=======================================================================
+
+.Table of constant parameters
+[width="100%"]
+|=======================================================================
+| Name         | Description                    | Range                 | Units
+| stem:[\gamma] | Boundary conditions using Nitsche method | stem:[[10]]      | 
+| stem:[\k_0] | Air conductivity     | stem:[1]      | 
+| stem:[\k_1] | Conductivity - internal walls | stem:[0.25]      | 
+| stem:[\k_2] | Conductivity - internal doors  | stem:[0.13]      |
+| stem:[\sigma]  | Heat transfer coefficient - front door | stem:[\frac{1.0}{0.06+\frac{0.06}{0.150}+\frac{0.1}{0.029}+0.14}] | 
+|=======================================================================

docs/mor/modules/ROOT/pages/thermalfin/index.adoc

@@ -0,0 +1,6 @@
+= Thermal fin
+:page-tags: case
+:page-illustration: pass:[toolboxes::wip/wip-1.svg]
+:description: Work in progress.
+
+The redaction of this page is in progress.

docs/mor/modules/ROOT/pages/toolboxmor.adoc

@@ -1,4 +1,7 @@
 = ToolboxMor
+:page-tags: manual
+:description: ToolboxMor manual
+:page-illustration: pass:[toolboxes::manual.svg]
 
 ToolboxMor is a class aiming to ease the use of the model order reduction framework of Feel++.
 Usually, you would need to define a class which would handle the initialization of the model, its affine decomposition and possibly the use of the EIM methods.

docs/user/modules/python/pages/pyfeelpp/filters.adoc

@@ -17,8 +17,18 @@ In this 2D and 3D example, we
 [%dynamic,python]
 ----
 import feelpp
-import sys
+import sys,os
+import spdlog as spd
+from feelpp.timing import tic, toc
+
+logger = spd.ConsoleLogger('Logger', False, True, True) 
+logger.set_level(spd.LogLevel.TRACE)
+
+tic()
 app = feelpp.Environment(["myapp"],config=feelpp.localRepository("")) # <1>
+toc("init Feel++")
+
+logger.info(f"Feel++ version: {feelpp.Info.version()}")
 ----
 <1> The {feelpp} environment is initiated with the name of the application and the path to the local repository where the results will be stored.
 
@@ -27,18 +37,23 @@ app = feelpp.Environment(["myapp"],config=feelpp.localRepository("")) # <1>
 app.setLogVerbosityLevel(0) # <1>
 geofilename=feelpp.download( "github:{repo:feelpp,path:feelpp/quickstart/laplacian/cases/feelpp2d/feelpp2d.geo}", worldComm=app.worldCommPtr() )[0]
 
+tic()
 mesh = feelpp.load(feelpp.mesh(dim=2,realdim=2), name=geofilename, h=0.1, verbose=1) # <2>
+toc("load mesh")
+logger.info(f"mesh loaded")
 
 Xh=feelpp.functionSpace(mesh=mesh,space="Pch",order=1) # <3>
 P0h=feelpp.functionSpace(mesh=mesh,space="Pdh",order=0) # <4>
 u=Xh.element() # <5>
 u.on(range=feelpp.elements(mesh), expr=feelpp.expr("sin(2*pi*x)*cos(pi*y):x:y")) # <6>
+logger.info(f"functionspace built and u created")
 
 e = feelpp.exporter(mesh=mesh)  # <7>
 e.add("a_scalar", 1.) # <8>
 e.add("u",u) # <9>
 e.add("pid",feelpp.pid( P0h )) # <10>
 e.save() # <11>
+logger.info(f"export done")
 ----
 <1> The verbosity level is set to 0 (only `VLOG(level)` with `level <= 0` are displayed)
 <2> The mesh is loaded from the {uri-github-feelpp} repository
@@ -70,12 +85,24 @@ def pv_get_mesh(mesh_path):
     mesh = reader.read()
     return mesh
 
-def pv_plot(mesh, field="u", clim=None, cmap='viridis', cpos='xy', show_scalar_bar=True, show_edges=True):
-    mesh.plot(scalars=field, clim=clim, cmap=cmap, cpos=cpos, show_scalar_bar=show_scalar_bar, show_edges=show_edges)
-
 plotter = pv.Plotter()
+plotter.show_axes()
 mesh = pv_get_mesh(f"exports/ensightgold/Exporter/Exporter.case")
 plotter.add_mesh(mesh, scalars="u", clim=None, cmap="viridis", show_scalar_bar=True, show_edges=True)
+plotter.camera_position = 'xy'
+axes = pv.create_axes_marker(
+                                line_width=4,
+                                ambient=0.0,
+                                x_color="#378df0",
+                                y_color="#ab2e5d",
+                                z_color="#f7fb9a",
+                                xlabel="X Axis",
+                                ylabel="Y Axis",
+                                zlabel="Z Axis",
+                                label_size=(0.1, 0.1), label_color="#aaaaaa",
+                            )
+plotter.add_actor(axes)
+
 plotter.show()
 ----
 

lib/dynamic-notebook.js

@@ -93,6 +93,7 @@ sys.stdout.write(plotter.export_html(None).getvalue())`)
               let source = response[index].stdout.toString('utf8')
               if (block.isOption('raw')) {
                 if (block.getAttribute('output') === 'pyvista') {
+                  logger.debug(source)
                   source = source.replace(pyvistaContainerRx, `var container = document.getElementById('pyvista-${index}')`)
                   source = source.replace(pyvistaFaviconRx, '')
                   const found = source.match(pyvistaScriptRx)

requirements.txt

@@ -2,4 +2,7 @@ pyvista
 xvfbwrapper
 ipykernel
 pythreejs
-plotly
+plotly
+trame-vtk
+trame
+spdlog

site-dev.yml

@@ -2,6 +2,9 @@ site:
   title: Feel++ // Docs
   url: https://docs.feelpp.org
   start_page: home::index.adoc
+runtime:
+  log:
+    level: debug
 content:
   sources:
   - url: ./
@@ -74,9 +77,9 @@ content:
   - url: ./
     branches: develop
     start_path: docs/salome/
-  - url: ../Antora/antora-ui
-    branches: mais
-    start_path: docs/
+#  - url: ../Antora/antora-ui
+#    branches: mais
+#    start_path: docs/
 #  - url: ./
 #    branches: mor-module
 #    start_path: docs/mor/