This is my presentation for OpenFOAM workshop 13 presentation, unfortunately, I can not attend the workshop in person.
Link to my presentation PDF:
OFW13-19-119__Coupling_OpenFOAM_with_FeniCS_for_multiphysis_simulation__QingfengXIA
Outline of this presentation:
1. physics simulation automation
2. CFD module for FreeCAD (GUI for OpenFOAM)
3. multiphysics coupling by OpenFOAM and FenicsSolver
4. Future plan
after windows 10 2018 april update, it is possible to run my CFD module on FreeCAD 0.17
Limited by my time I can spend on this open source project, I will will make new feature in about half year, but maintain CFD module working with Stable FreeCAD release.
This is also announced in Fenics support forum
Screenshot of FenicsSolver in FreeCAD
Dear all,
I have developed several multi-physics solver based on Fenics, it is hosted on github:
https://github.com/qingfengxia/FenicsSolver
This solver is data driven (json), instead of programming for every case. It is still in early stage, I would pick up advice from community, especially standardization of json input data format, naming.
It is primarily used as a submodule for my CFD workbench for FreeCAD, giving GUI for boundary selection. I think a GUI for boundary selection is crucial for complicate geometry. I also use it for other projects with maximum code re-usage.
https://github.com/qingfengxia/Cfd
My future plan will be integrate Fenics with OpenFOAM which is quite advanced in multiphase flow and turbulent flow. Recently, my time is very limited without a permanent position in the academia, thus my update and response will be slow.
I should attend Fenics 2018 at Oxford to demonstrate some advanced usage.
Thanks
Qingfeng Xia @ Engineering Science Dept of Oxford University
Recently relised visual studio build tool (with cmake support), enables building windows c++ project without GUI. It is essential to accelerate the testing of cross-platform program.
It is convenient and decent to add Bash (WSL) and visual studio command line tool
1. git clone
2. cd source & mkdir build & cd build & cmake .. # cmake to generate msbuild/makefile
3. nmake # to compile
It is absolutely possible – what you probably want to do is create a “bare” git repository in folder Y (git init --bare)
and then add that file location as a remote:
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git remote add Y file:///path/to/Y #example path: file:///media/sf_OneDrive/gitr<wbr />epo/FenicsSolver/ |
======= push and pull has different repo ==========
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git remote set-url origin --push --add <a remote> git remote set-url origin --push --add <another remote></code><code> |
========push to multiple repo======
The latest version of git (as of October 2012) allows you to do this from the command line:
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git remote set-url origin --push --add user1@repo1 git remote set-url origin --push --add user2@repo2 git remote -v |
It is also possible to push encrypted code to public repo, not tested.
Precise control of the thickness of the first cell normal to wall, is crucial for turbulence models like k-epsilon, k-omega. Before moving to turbulence flow simulation for CFD workbench of FreeCAD
2D meshing with boundary layer, tutorial
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from dolfin import * import os.path from subprocess import Popen, PIPE, check_output # https://fenicsproject.org/qa/9983/setting-boundary-conditions-for-meshes-generated-by-gmsh # generete mesh by: gmsh test.geo -3 # dolfin-convert -i gmsh test.msh test.xml geo_file_content = """ size = 1; //m meshThickness = size / 3; gridsize = size / 5; // All numbering counterclockwise from bottom-left corner Point(1) = {0, 0, 0, gridsize}; Point(2) = {0, size, 0, gridsize}; Point(3) = {size, size, 0, gridsize}; Point(4) = {size, 0, 0, gridsize}; Line(1) = {1, 2}; Line(2) = {2, 3}; Line(3) = {3, 4}; Line(4) = {4, 1}; Line Loop(4) = {1, 2, 3, 4}; Plane Surface(8) = {4}; Physical Line(12) = {1}; Physical Line(23) = {2}; Physical Line(34) = {3}; Physical Line(41) = {4}; Physical Surface(1) = {8}; // do not comment out this line //Transfinite Surface{8}; // fenics does not support recomine //Recombine Surface{8}; // boundary layer Field[4] = BoundaryLayer; Field[4].EdgesList = {1,3}; // FacesList for 3D Field[4].hfar = 10; Field[4].hwall_n = 0.015; Field[4].hwall_t = 0.01; Field[4].thickness = 0.02; Field[4].ratio = 1.0; BoundaryLayer Field = 4; Mesh.CharacteristicLengthFromCurvature = 1; Mesh.Algorithm = 8; // delannay=1 """ fname="test" with open(fname+".geo", 'w') as f: f.write(geo_file_content) cmd = 'gmsh {}.geo -3'.format(fname) print check_output([cmd], shell=True) # run in shell mode in case you are not run in terminal cmd = 'dolfin-convert -i gmsh {}.msh {}.xml'.format(fname, fname) Popen([cmd], stdout=PIPE, shell=True).communicate() mesh = Mesh(fname+".xml") if os.path.exists( fname+"_physical_region.xml"): subdomains = MeshFunction("size_t", mesh, fname+"_physical_region.xml") plot(subdomains) if os.path.exists( fname+"_facet_region.xml"): boundaries = MeshFunction("size_t", mesh, fname+"_facet_region.xml") plot(boundaries) plot(mesh) interactive() |
Fenics geometry building API is based on CGAL, it can import CAD, but can not export CAD file like step. Here is a solution, not fully tested. This file may be further developed in github.
for any expression in Expression for Fenics 2016.2( installed from PPA )
expr = """ x[2]> {} ? {}:{}""".format(disc_zmax, lambda_p, lambda_d)
print(expr)
K = Expression(expr, element=V.ufl_element()) # error in compiling
instant error log:
”
— The imported target “vtkRenderingPythonTkWidgets” references the file
“/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so”
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
“/usr/lib/cmake/vtk-6.2/VTKTargets.cmake”
but not all the files it references.
”
check if this file is missing or not
ls -l /usr/lib/python2.7/dist-packages/vtk/libvtkRendering*
python-vtk6 (VTK6.2) is installed, and installed file list:
/usr/lib/python2.7/dist-packages/vtk/libvtkRenderingPythonTkWidgets.x86_64-linux-gnu.so
sudo ln -s /usr/lib/python2.7/dist-packages/vtk/libvtkRenderingPythonTkWidgets.x86_64-linux-gnu-6.2.so /usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so
#this is the only file needs symbolic link to /usr/lib/x86_64-linux-gnu/
then, error is solved
#Cmake cheat sheet in markdown
size_t which is unsigned int to represent size of containters like std::vector, std::stringinclude <stdint.h> and use int64_twarning: comparison between signed and unsigned integer expressions [-Wsign-compare] . However, mixed unsigned and signed int algorithm is not warnedctypes module defined c++ unsigned types; python 3 integer will not overflowhttp://blog.robertelder.org/signed-or-unsigned-part-2/
example and explanation from stackoverflow
10 Many binary operators that expect operands of arithmetic or enumeration type cause conversions and yield result types in a similar way. The purpose is to yield a common type, which is also the type of the result. This pattern is called the usual arithmetic conversions, which are de?ned as follows:
2 clauses about equal types or types of equal sign omitted
comparison of unsigned expression >= 0 is always true [-Wtype-limits]
see more c and c++ pitfalls
-0.5 < x < 0.5Guru of the Week (GotW) is a series of C++ programming problems created and written by Herb Sutter.
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#include <iostream> #include <limits> #include <vector> void std_container_test(){ std::vector<int> v; int i = 10; if (i < v.size()-1) // there is a compiler warning here std::cout <<"underflow occurs for empty container size()-1\n"; } void underflow_test(int input_s, unsigned int input_u){ unsigned int size_u = 10u; unsigned int i_u; int size_s = 10; int i_s; // infinite looping for underflow for(i_u = size_u -1; i_u >=0; i_u--){ std::cout <<"unsigned: " << ((input_u + i_u) / 2u) << "\n"; } } void float_overflow_test() { float d = std::numeric_limits<float>::max(); std::cout << "std::numeric_limits<float>::max() = " << d << std::endl; float q = d + 100; //behavior is undefined, could be inf, or remained as std::numeric_limits<float>::max() std::cout << "q: " << q << std::endl; } void bool_implicit_coversion_pitfall_test() { int x = 0; if (!(-0.5 <= x <= 0.5)) std::cout << "x=0, -0.5 <= x <= 0.5 is false"<<"\n"; } void signed_int_test() { signed int s1 = -4; unsigned int u1 = 2; signed long long s2 = -4; unsigned int u2 = 2; signed long long int s3 = -4; unsigned long int u3 = 2; unsigned long int u4 = -2; // no worning at all if (s1>u1) std::cout << s1 << " > " << u1 << " is true? \n"; std::cout << (s1 + u1) << "\n"; // 4294967294 std::cout << (s2 + u2) << "\n"; // -2 std::cout << (s3 + u3) << "\n"; // 18446744073709551614 std::cout << " What are you expecting from `unsigned long int u4 = -2;`, actually stored integer is " << u4<< "\n"; } int main() { signed_int_test(); bool_implicit_coversion_pitfall_test() ; std_container_test(); float_overflow_test(); } |
Introducing the Visual Studio Build Tools
“If you have installed Microsoft Visual C++ Build Tools 2015 on Windows 10, open the Start menu and choose All apps. Scroll down and open the Visual C++ Build Tools folder. Choose Visual C++ 2015 x86 Native Tools Command Prompt to open the command prompt window.”
1) for single file source file
cl -> gcc , but the command options is different,
cl /EHsc hello.cpp
https://msdn.microsoft.com/en-us/library/f35ctcxw.aspx
2) for a small project, CMake is recommended,
it is handy to write one from example CMakeLists.txt online.
In your source code folder: md build && cd build && cmake ..
then using nmake instead of make
3) for exsitent vs solution using msbuild:
compile visual studio solution/project designed by VS IDE, no corresponding command on Linux.
search “MSBuild Command-Line Reference”
In the near future, other light weight IDE might support detecting “Visual Studio Build Tools”, e.g QtCreator
1. install shafa TV manager and/or ES file explorer to be enable install apk from USB/SD card
http://www.shafa.com/articles/yWNpNK6erhB6Q4dO.html
2. install Kodi/XMBC apk from shafa’s file manager (in toolbox) on USB storage
3. install apk of youtube for Google TV, and also enable USB keyboard in MiBox system setting -> Input.
3. enable DNLA, web http control, UPnP in kodi settings
http://kodi.wiki/view/web_interface
write down the IP (check on your router), port, user name and password on this setting page
For web http control, install the new “Chorus” theme addon
4. install “play to Kodi” Chrome extension, Firefox should be possible
then, right click to video link, kodi->play/queue
first of all, setup kodi extension to login to kodi web interface
5. disable screen saver, for Kodi
## installation
After Anniversary Build (2016 Aug) for x65 windows 10, it is possible to evaluate this beta feature in developer mode without upgrade to claimed unstable insider version.
see detailed tutorial:
To install ubuntu on windows 10 from power shell prompt:
Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux
## overview
In addition to apt-get, some other tool are there like python2, and python3, gcc4.9, perl5. dbus, systemd
Xwindows has been explored by geeks, but it is not stable/usable to run GUI app.
After fireup bash, the current path is /mnt/c/Windwos/System32 . It is better to “cd /mnt/c/.bashrc, not mess up system folder and for better locate file generated by bash commands.
## look around
– dpkg -l to see installed package, while not sure snap pkg will be supported.
– sudo apt-get update To update the repo, it will show trusty repo info
– ls /dev/
– ls /usr/include/, almost empty
– lsb_release -a shows it is 14.04.4
– uname -a
> Linux DESKTOP-DELL15 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 GNU/Linux
## test POSIX API
It may be used to easily run software previously POSIX only program on windows.
apt-get install gcc will install gcc 4.8 and *linux-libc-dev*
ls /usr/include/ will give unistd.h
## install OpenFOAM
see instruction:
two versions are available for ubuntu 14.04
openfoam30
openfoam4
OpenMPI may not work; ParaView is definetly not working.
apt-get install openfoam30, then apt-get remove openfoam30 (leave dependent pkg remained.)
install openfoam4 by force, will not install all paraview related tons of new packages.
apt-get download openfoam4
dpkg --force-all -i openfoam4
force remove this pkg can fix error message each time
## Run OpenFOAM solver
mkdir -p $FOAM_RUN
cp -r $FOAM_TUTORIALS $FOAM_RUN
cd $FOAM_RUN/tutorials
bash
/OpenFOAM/qingfeng-4.0/incompressible/simpleFoam/windAroundBuildings$ ./Allrun
Running surfaceFeatureExtract on /home/qingfeng/OpenFOAM/qingfeng-4.0/incompressible/simpleFoam/windAroundBuildings
Running blockMesh on /home/qingfeng/OpenFOAM/qingfeng-4.0/incompressible/simpleFoam/windAroundBuildings
Running snappyHexMesh on /home/qingfeng/OpenFOAM/qingfeng-4.0/incompressible/simpleFoam/windAroundBuildings
Running simpleFoam on /home/qingfeng/OpenFOAM/qingfeng-4.0/incompressible/simpleFoam/windAroundBuildings
## Feature wanted
– right click to open bash, just as cmd prompt, or git-bash
## upgrade to ubuntu 16.04
upgrade to ubuntu 16.04 is planned by official support
apt-get update
apt-get dist-upgrade
do-release-upgrade -f DistUpgradeViewNonInteractive -d
lxrun.exe is used to manage WSL. This command can be used to install or uninstall the Ubuntu image.
UPDATE: it seems the following methods still fails, as restart pc or windows update will invalidated the setting
===========
Avoid the annoying hotkey to trigger the IME shape/punctation in Chinese for half/full
see tutorial: http://superuser.com/questions/327479/ctrl-space-always-toggles-chinese-ime-windows-7
In addition to disapble Ctrl-Space, IME shape/punctation hotkeys are also disabled, which are shift-space and ctrl-period respectively. Once your edit the hotkey in GUI, which you will fail, you may need to rerun this reg file again. Logout to make it take effect
copy the following into notepad and save as “diasableIMEHotkey.reg” to anywhere in your PC. right click “merge” will import them into registry.
[HKEY_CURRENT_USER\Control Panel\Input Method\Hot Keys\00000010] for simplified Chinese, for traditional Chiese, use : [HKEY_CURRENT_USER\Control Panel\Input Method\Hot Keys\00000070]
Once your edit the hotkey in GUI, which you will fail, you may need to rerun this reg file again. Logout to make it take effect
user space library libiio (https://wiki.analog.com/resources/tools-software/linux-software/libiio)
#include <iio.h> four basic classes: iio_contex, iio_device, iio_channel and iio_bufferiio_trigger is kind of iio_device without channel but with name inc “trigger”iio_context has internal operation functions structure, kernel driver(http://events.linuxfoundation.org/sites/events/files/slides/lceu15_baluta.pdf) + scan_element(), iio_channel_is_scan_element(): elements in buffer is called scan /sys/bus/iio/devices/iio:devices/scan elements
trigger readings based on an external interrupt source hardware interrupt (IRQ pins) software interrupts (periodic timers, sysfs triggers)
(linux/iio/triggered_buffer.h);trigger are software trigger, not hardware TTL signal in DAQ terminology?libiioAbout 200 device drivers by the time of kernel 4.4; many drivers supports a varierty of models.
see/search kernel source tree linux/iio, there are a few subfolders corresponds to sensor categories: “ADC, DAC, light, accel(erometer), gyro, magnetometer, humidity, temperature, amplifier, frequency, orientation, health”, etc
“dummy” a virtual sensor for testing
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sudo apt-get install libiio libiio-dev libiio-python libiio-utils <span class="hljs-comment">#all trigger related function need kernel module to support</span> sudo modprobe iio_dummy iio_info ls /sys/bus/iio/devices/iio\<span class="hljs-symbol">:device0</span> cat /sys/bus/iio/devices/iio\<span class="hljs-symbol">:device0/name</span> <span class="hljs-comment">#no need to enable?</span> cat /sys/bus/iio/devices/iio\<span class="hljs-symbol">:device0/in_accel_x_raw</span> |
for office system, I recommend kingsoft WPS office, which is based on Qt, much faster than java based solution. It has Android, Linux version in alpha, in addition to mature windows ‘s version
http://wps-community.org/download.html
For 2D CAD drawing, I recommend Dassault system’ Draftsight, it is a professional level product. just need a email activation. Linux version is still in beta.
http://www.3ds.com/products-services/draftsight-cad-software/free-download/
Both are not open source, but free of charge for production usage.
Updated 2016-04-17
Boundary condition setup GUI has been done for preview
This is an early preview, only for people with experience of OpenFoam.
Test instruction could be found at
https://github.com/qingfengxia/FreeCAD/ … /Readme.md
I would love to see some feedback for stage III development, see roadmap:
https://github.com/qingfengxia/FreeCAD/ … roadmap.md
A video preview of OpenFoam plugin for FreeCAD Fem workbench
http://www.iesensor.com/FreeCADDoc/oepn … engXIA.mp4
The discussion of this module on FreeCAD community can be found here:
http://forum.freecadweb.org/viewtopic.php?f=18&t=13699
