mearg with development branch

openworm · Jul 28, 2015 · c48fb40 · c48fb40
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diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,6 @@
-/release/Smoothed-Particle-Hydrodynamics
+/src/main_sim.py~
+/Release/Sibernetic
+*~
 # Compiled Object files
 *.slo
 *.lo

diff --git a/README.md b/README.md
@@ -1,36 +1,34 @@
 ![Sibernetic](http://i.imgur.com/Hbsw6Zs.png)
 
-Sibernetic is a fluid mechanics simulator developed for simulations of C. elegans developed for the [OpenWorm](http://openworm.org) project by Andrey Palyanov, Sergey Khayrulin and Mike Vella as part of the [OpenWorm team](http://www.openworm.org/people.html). Sibernetic provides an implementation of the PCISPH contractile matter algorithm for simulating muscle tissue and is being applied to C. elegans locomotion.
+Sibernetic is a fluid mechanics simulator developed for simulations of C. elegans in the [OpenWorm project](http://www.openworm.org) developed for the [OpenWorm](http://openworm.org) project by Andrey Palyanov, Sergey Khayrulin and Mike Vella as part of the [OpenWorm team](http://www.openworm.org/people.html). Sibernetic provides an implementation of the PCISPH contractile matter algorithm for simulating muscle tissue and is applies to C. elegans locomotion.
 
-When driven by electrical activity generated by simulated neurons using the [Hodgkin Huxley model](https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model) contractile matter is called Electrofluid (this feature is in the early stages of development).
+When driven by [Hodgkin Huxley dynamics](https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model) contractile matter is called Electrofluid.
 
-Sibernetic is primarily written in  C++ and OpenCL, and also features interaction with Python scripts.
+Sibernetic is primarily written in  C++ and OpenCL, it also provides a Python API.
 
-There is a separate effort lead by [Giovanni Idili](https://github.com/gidili) and [Sergey Khayrulin](https://github.com/skhayrulin) to port this code to Java, as part of the [Geppetto simulation framework](http://docs.geppetto.org/en/latest/). 
+There is a separate effort lead by [Giovanni Idili](https://github.com/gidili) and [Sergey Khayrulin](https://github.com/skhayrulin) to port this code to Java, as part of the [Geppetto simulation framework](https://github.com/openworm/OpenWorm/wiki/Geppetto--Overview). 
 
 Compiling / running (Linux/mac)
 ------------------------------
 
 **Linux**
 
-Install OpenCL on Ubuntu. We suggest you initially go with [AMD OpenCL drivers](http://developer.amd.com/tools-and-sdks/heterogeneous-computing/amd-accelerated-parallel-processing-app-sdk/downloads/) as we have found these to be the most stable and complete. You can also try [Intel's drivers](http://develnoter.blogspot.co.uk/2012/05/installing-opencl-in-ubuntu-1204.html). This step often causes problems, contact the [openworm-discuss](https://groups.google.com/forum/#!forum/openworm-discuss) mailing list if you encounter issues, or check [here](https://github.com/openworm/Smoothed-Particle-Hydrodynamics/issues). The AMD drivers include samples in /opt/AMDAPP/samples/opencl/bin which you can use to verify your OpenCL support is working.
+Install OpenCL on Ubuntu. We suggest you initially go with [AMD OpenCL drivers](http://developer.amd.com/tools-and-sdks/heterogeneous-computing/amd-accelerated-parallel-processing-app-sdk/downloads/) as we have found these to be the most stable and complete. You can also try [Intel's drivers](http://develnoter.blogspot.co.uk/2012/05/installing-opencl-in-ubuntu-1204.html). This step often causes problems, contact the [openworm-discuss](https://groups.google.com/forum/#!forum/openworm-discuss) mailing list if you encounter issues. The AMD drivers include samples in /opt/AMDAPP/samples/opencl/bin which you can use to verify your OpenCL support is working.
 
 You'll also need a variety of libraries. In ubuntu, install the dependencies with:
 
 ```
 sudo apt-get install g++ python-dev freeglut3-dev nvidia-opencl-dev libglu1-mesa-dev libglew-dev python-numpy
 ```
 
-When these are installed run:
+Next, navigate to the `Release` folder and run:
 
 ```
 make clean
 make all
 ```
 
-**Mac**
-
-From the top-level folder and run:
+**Mac**: stay in the top-level folder and run:
 
 ```
 make clean -f makefile.OSX
@@ -53,7 +51,7 @@ g++ -L/usr/lib -L/usr/lib/python2.7 -o "Smoothed-Particle-Hydrodynamics"  ./src/
 Finished building target: Smoothed-Particle-Hydrodynamics
 ```
 
-Set your `PYTHONPATH`:
+Then navigate to the top-level folder in the hierarchy (e.g `Smoothed-Particle-Hydrodynamics`) and set your `PYTHONPATH`:
 
 ```
 export PYTHONPATH=$PYTHONPATH:'./src'
@@ -85,6 +83,7 @@ Compilation failed:
 #include "src//owOpenCLConstant.h"
 ```
 
+
 What's inside
 -------------
 
@@ -108,6 +107,91 @@ References
 2. M. Ihmsen, N. Akinci, M. Gissler, M. Teschner, Boundary Handling and Adaptive Time-stepping for PCISPH Proc. VRIPHYS, Copenhagen, Denmark, pp. 79-88, Nov 11-12, 2010.
 3. M. Becker, M. Teschner. Weakly compressible SPH for free surface flows // Proceedings of the 2007 ACM SIGGRAPH/Eurographics symposium on Computer animation, pages 209-217.
 
+Main command options
+--------------
+To start Sibernetic with argument print in command prompt next ./Release/Sibernetic -whatever
+Available options:
+```
+ -g_no                 Run without graphics
+ -l_to                 Save simulation results to disk.
+ -l_from               Load simulation results from disk.
+ -test                 Run some physical tests.
+ -f <filename>         Load configuration from file ./configuration/<filename>.
+ device=<device_type>  Trying to init OpenCL on device <type> it could be cpu or gpu 
+                       default-ALL (it try to init most powerful available device).
+ timestep=<value>      Start simulation with time step = <value> in seconds.
+ timelimit=<value>     Run simulation until <value> will be reached in seconds.
+ leapfrog              Use for integration LeapFrog method
+ -help                 Print this information on screen.
+```
+
+LeapFrog integration
+--------------
+[Leapfrog](https://en.wikipedia.org/wiki/Leapfrog_integration) is second order method insted of [Semi-implicid Euler](https://en.wikipedia.org/wiki/Semi-implicit_Euler_method) which we are using as default method for integration. For run simulation with Leapfro integration medhod print run command
+```
+./Release/Sibernetic leapfrog
+```
+
+Run simulation from configuration file
+--------------
+All configuration is stored in ./configuration folder there are two demo configuration demo1 and demo2 (demo1 is using as default demonstarative configuration). You can switch between two demo configurations directly inside the working Sibernetic - just push button '1' or '2' respectively. For run your configuration put you're configuration file into configuration folder and run Sibernetic with key 
+```
+./Release/Sibernetic -f <configuration_file_name>. 
+```
+For run worm body simulation you should run Siberntic with key 
+```
+./Release/Sibernetic -f worm
+```
+it load worm body simulation and run pyhon modul which is responsible for muscle signal updating. If you want work with worm body configuration generator you should change branch to WormBodySimultion.
+
+Control in graphical mode
+---------------
+If you run Sibernetic with graphic you can work with scene rotate and scaling by mouse. Also you several control button is available:
+```
+'Space' - pause simulation 
+'s'     - save current configuration into file ./configuration/snapshot/configuration_default you can run this
+than (./Release/Sibernetic -f /snapshot/configuration_default).
+'q' or 'Esc'     - quit the semulation 
+'1'     - run demo1 configuration
+'2'     - run demo2 configuration
+```
+
+Configuration file format
+---------------
+Configuration file is consist from:
+```
+First 6 lines is spatial description of boundary box
+xmin
+xmax
+ymin
+ymax
+zmin
+zmax
+[position] - contains information about position of all particles e.g.
+1 0 0 1
+1 0 0 1
+...
+[velocity] - contains infomation about velocityes of all particles e.g.
+0 0 0 1
+0 0 0 1
+...
+[connection] - contains infomation about elastic connection of all elastic particles e.g.
+1	1.58649939377	1.1	0.0
+7	1.58649939377	1.1	0.0
+...
+[membranes] - contains infomation about membranes e.g.
+0	1	7
+7	8	1
+...
+[particleMemIndex] - contains infomation about in which membranes elastic particle is includes e.g.
+0
+144
+288
+-1
+...
+```
+
+
 Saving to disk
 --------------
 You can run Sibernetic on gpu for this you should start Sibernetic with key device=gpu.

diff --git a/Sibernetic.vcproj b/Sibernetic.vcproj
@@ -2,7 +2,7 @@
 <VisualStudioProject
 	ProjectType="Visual C++"
 	Version="9.00"
-	Name="SimulationEnginePrototype"
+	Name="Sibernetic"
 	ProjectGUID="{01EA498F-06C1-4F67-8B98-E1105F9311A2}"
 	RootNamespace="SimulationEnginePrototype"
 	Keyword="Win32Proj"
@@ -61,6 +61,8 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
+				OutputFile="$(OutDir)\$(ProjectName).exe"
+				Version="0.0.1"
 				LinkIncremental="2"
 				AdditionalLibraryDirectories="&quot;lib/$(PlatformName)&quot;"
 				GenerateDebugInformation="true"
@@ -135,6 +137,8 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
+				OutputFile="$(OutDir)\$(ProjectName).exe"
+				Version="0.0.1"
 				LinkIncremental="1"
 				AdditionalLibraryDirectories="C:\Python25\libs;&quot;lib/$(PlatformName)&quot;"
 				GenerateDebugInformation="true"
@@ -210,6 +214,8 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
+				OutputFile="$(OutDir)\$(TargetName).exe"
+				Version="0.0.1"
 				LinkIncremental="2"
 				AdditionalLibraryDirectories="&quot;lib/$(PlatformName)&quot;"
 				GenerateDebugInformation="true"
@@ -264,13 +270,21 @@
 				>
 			</File>
 			<File
-				RelativePath=".\src\owWorldSimulation.cpp"
+				RelativePath=".\src\test\owPhysicTest.cpp"
 				>
 			</File>
 			<File
 				RelativePath=".\src\test\owPhysicTest.cpp"
 				>
 			</File>
+			<File
+				RelativePath=".\src\owWorldSimulation.cpp"
+				>
+			</File>
+			<File
+				RelativePath=".\src\PyramidalSimulation.cpp"
+				>
+			</File>
 			<File
 				RelativePath=".\src\sphFluid.cl"
 				>
@@ -315,16 +329,24 @@
 				RelativePath=".\inc\owPhysicsFluidSimulator.h"
 				>
 			</File>
+			<File
+				RelativePath=".\inc\owPhysicTest.h"
+				>
+			</File>
 			<File
 				RelativePath=".\inc\owWorldSimulation.h"
 				>
 			</File>
+			<File
+				RelativePath=".\inc\PyramidalSimulation.h"
+				>
+			</File>
 			<File
 				RelativePath=".\inc\VectorMath.h"
 				>
 			</File>
 			<File
-				RelativePath=".\inc\owPhysicTest.h"
+				RelativePath=".\inc\owConfigProperty.h"
 				>
 			</File>
 		</Filter>