LubricationCorrections

Fast algorithms for applying lubrication corrections to fluctuating suspensions of spherical particles above a bottom wall

Prerequisites

In order to run the code, the SuiteSparse library must be installed on the system http://faculty.cse.tamu.edu/davis/suitesparse.html

In Ubuntu 18, this can be accomplished by running sudo apt install libsuitesparse-dev

C++ dependencies

Additionally, the C++ libraries Boost and Eigen must be installed Ensure that the verion of Boost is >= 1.64

In Ubuntu 18, these libraries can be installed by running, e.g.

sudo apt install libeigen3-dev
sudo apt install libboost1.67-all-dev

Python dependencies

In addition, the following python packages must be installed via pip

pip install --user scipy
pip install --user pyamg
pip install --user scikit-sparse

Makefile

To run the code, one needs to Make the C++ helper code in the directory /Lubrication

https://github.com/stochasticHydroTools/LubricationCorrections/tree/master/Lubrication

To ensure the Makefile functions properly,

Change lines

LubricationCorrections/Lubrication/Makefile

Lines 9 to 10 in eb60857

	BOOST_INC = /usr/include/boost
	BOOST_LIB = /usr/lib64

to reflect the location of Boost on your system, and change line

LubricationCorrections/Lubrication/Makefile

Line 12 in eb60857

EIGEN_INC = /usr/local/include/eigen3

to relect the location of the Eigen Include directory on your system.

NOT TESTED: If python3 is to be used, change to -lboost_python3 -lboost_numpy3 in line

LubricationCorrections/Lubrication/Makefile

Line 26 in eb60857

g++ -O3 -shared -dynamiclib $(TARGET).o -L$(BOOST_LIB) -lboost_python -lboost_numpy -L$(PYTHON_LIB) -lpython$(PYTHON_VERSION) -o $(TARGET).so

Test

To test the the C++ helper function run properly, simply run

python test.py 

after a sucessful make in the /Lubrication directory. If this code produces output, then things are working as they should.