A simulation of the mechanics of a surface as a 2D or 3D set of (visco-) elastic springs.
In a terminal, run :
$ ./plyssim config.yamlIn which config.yaml is an appropriate config file.
First install the required libraries/packages.
Open a terminal, then clone/download code in directory <DIR> :
$ git checkout https://github.com/SergeDmi/Plyssim.git <DIR>
$ cd <DIR>Then run the compilation script :
$ ./setupIf any error happens at compile time, this is probably a compilation error and you should check if required packages are indeed installed, then check the options in the CMakeLists.txt.
For this you might need to install make, cmake, gcc and the openmp and boost libraries. To do so on Ubuntu, write in a terminal :
$ sudo apt-get install make cmake g++
$ sudo apt-get install libboost-all-devOn a Mac, you can use brew install if you are using Homebrew as your package manager. In a terminal, write :
$ brew install boost
$ brew install cmake
$ brew install libompI would recommend using clang as a C++ compiler.
$ brew install llvmYou may find online resources on how to set up compiler variables for cmake to use clang, for example here.
On Windows, you can install Ubuntu on a virtual machine, see this tutorial for instance. You can also directly compile and run on windows if you like to make your life difficult.
Config files are yaml type. See config.yaml for an example.
Here is another simple config file
meshes:
first:
source: demo.ply
type: 1
power_law: 2
prestrain: 1.0
k_elast: 1.0
another:
source: demo.ply
prestrain: 1.1
k_elast: 1.0
runs:
deflated:
duration: 500
n_frames: 5
dt: 0.005
pressure: 0.0
confinement:
y:
min: -2.2
max: 2.2
stiffness: 40
inflated:
pressure: 1.0Here, first,another are two meshes we want to simulate. Each mesh will be simulated in two runs (deflated and inflated). For meshes and runs, any name will do. Even Meshuggah.
Here MESH and RUN are the name specified for a given mesh and run, e.g. another is the name of the second mesh, while deflated is the name of the first run, in the example above. Plyssim does not have an imposed unit system, so Make sure you are using consistent units throughout.
MESH.source : source file (ex : demo.ply, or bla/bli/blo.ply)
MESH.type : type of meshwork (1: 2D, 3: 2D+bending, 4: Tetrahedral 3D mesh)
MESH.power_law : power law of spring elasticity (1, 2 or 3)
MESH.prestrain : prestrain of the springs in the ply file (ex : 1.0 for no prestrain, 1.5 for 50% prestrain)
MESH.k_elast : sping constant (not required if young_modulus and thickness are given, in physical units).
MESH.young_modulus : Young modulus of the mesh. Overides k_elast and requires thickness.
MESH.thickness : Virtual thickness of the mesh - used to compute k_elast from young_modulus.
MESH.k_bending : Bending rigidity of the mesh (in units of energy, e.g. MPa x µm^3). Only for type=3. Default value computed from young_modulus, thickness, and poisson.
MESH.poisson : Poisson ratio of the surface, used to compute k_bending from young_modulus and thickness, only for type=3.
MESH.viscosity : Viscosity of the medium around the mesh (in physical units, e.g. MPa x seconds).
MESH.out : base name for exported ply files.
MESH.verbose : toggles extra reports on the mesh (0 or 1).
RUN.duration : duration of run (in physical time, e.g. seconds)
RUN.n_frames : number of exported time frames
RUN.dt : simulation timestep (in physical time)
RUN.pressure : pressure in the cell (in physical units, e.g. MPa)
RUN.confinement.AXIS : Confinement on axis AXIS=x,y,z
RUN.confinement.AXIS.min : lower confinement bound (in physical distance e.g. µm)
RUN.confinement.AXIS.max : higher confinement bound
RUN.confinement.AXIS.stiffness : confinement stiffness (in physical units, e.g. MPa/µm)
Format should be plain text or binary ply files. See demo.ply for an example. To quickly alter ply files (i.e. scale, rotate, center...), you can use the python-based tool ply_convert. Assuming you have Python3 with easy-install, just type :
$ pip3 install ply_convertSee ply_convert on PyPI for more information.
The program outputs ply files of the format NAME_RUN_TIME.ply, in which NAME is the name of the mesh provided in the config file (or the export name if given), RUN is the name of the run, and T is the time frame number.
Plyssim compiled succesfully with gcc, clang and icc (see CMakeLists.txt). Fastest executable was found to be with gcc, until clang caught up. So use your favorite (icc seems really slow though). Thanks gcc & llvm devs for the amazing work !
Plyssim is distributed under GNU GLP V3.0, see LICENCE. Plyssim links to Aboria, Tinyply, Yaml-cpp, that are public domain open source software.