Instructions for Ubuntu: (1) To run this code you need Eigen, OpenGL, Lapack, libtensorflow and cppflow.
Lapack is usually preinstalled on your computer. Eigen can be found at http://eigen.tuxfamily.org/index.php?title=Main_Page For libtensorflow and cppflow installation, please refer to https://serizba.github.io/cppflow/
(2) Make sure to change the path of the trained model is defined as a full path within your local directory. The model path change needs to be done in world.cpp file. Trained models are included in "/Translation" and "/Rotation" folder.
(2) Create a file named "Makefile". The content of the "Makefile" should be the same "Makefile" except that you will need to change the path to eigen, path to libtensorflow, and path to cppflow from the existing Makefile sample shown in this code to the local path of system.
(3) Open a terminal, "cd" to this folder and run the command "make" (without the quotes).
(4) To start the simulation, run the command "./MLRFT optionMLRFT_Translation.txt" (without the quotes). More on option.txt below.
(1) Angular/Linear velocity: a text file, e.g. omega.txt, should contain two columns: one column is the start time and second column is the angular velocity (rpm) or linear velocity (m/s). This is essentially the time series of the angular/linear velocity.
(2) The name of this input file should be specified in "option.txt" file under the option name "input-file". This option.txt should be specified while running the simulation, i.e. ./MLRFT option.txt
(3) You can edit the parameters of the simulation by editing "option.txt" file. You can also specify an option using the following syntax: ./MLRFT option.txt -- option_name option_value Example: ./MLRFT option.txt -- RodLength 0.2
(4) Details on the options (we use SI units):
"helixradius" is the radius of the helix.
"helixpitchRatio" is the value of helixpitch / helixradius.
"rodRadiusRatio" is the value of helixradius / rodRadius.
"contourRatio" is the value of flagellaLength / helixradius.
"youngM" is the young's modulus.
"Poisson" is the Poisson ratio.
"deltaTime" is the time step size.
"totalTime" is the time at which the simulation ends.
"tol" and "stol" are small numbers used in solving the linear system. Fraction of a percent, e.g. 1.0e-3, is often a good choice.
"maxIter" is the maximum number of iterations allowed before the solver quits.
"maxIterContact" is the maximum number of iterations allowed before the contact exits the loop.
"density" is the mass per unit volume.
"gVector" is the vector specifying acceleration due to gravity.
"viscosity" is the viscosity of the fluid medium.
"render" (0 or 1) indicates whether OpenGL visualization should be displayed.
"saveData" (0 or 1) indicates whether the location of the head should be saved in "datafiles/" folder (this folder will be created by the program).
"input-file" is the name of the file that provides the time series of angular/translational velocity (as mentioned above).
"use-RSS" is a boolean variable. If true, RSS will be used.
"use-RFT" is a boolean variable. If true, RFT will be used. See "Propulsion of microorganisms by a helical flagellum" for expressions of eta_par and eta_per in Gray and Hancock model.
* if both "use-RSS", and "use-RFT" are false, then MLRFT is activated
"translation" is a bollean variable. If true translation will be active. The input-file needs to be in m/s of translation. If false, rotation will be active and requires corresponding input-file.
"include-contact" is a boolean variable. If true, contact will be included. Otherwise, contact will be neglected.