Calculate position-dependent diffusivity functions from trajectory data (usually from molecular dynamics). The approach is described in http://doi.org/10.1021/ct300867e . The fractional Smoluchowski model is described in http://doi.org/10.1038/srep35913 .
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Examples
Bin.H
CommandLineReader.H
CrankNicholsonSolver.H
CrankNicholsonSolver1.H
DiffusionFusion.H
Event.H
Field.H
FieldDesc.H
FoxFunc.H
HistoryReader.H
LICENSE
Makefile
MetroMonteCarlo.H
Piecewise1d.H
PiecewiseBicubic.H
PiecewiseCubic.H
PiecewiseLinear.H
PiecewiseZero.H
Prior.H
README.md
RandomGsl.H
SmoluchowskiSolver.H
SolutionStruct.H
TimeFracCrankSolver.H
TimeFracCrankSolverFaster.H
TrajBdSmoluchowski.H
TrajComer.H
TrajComer2d.H
TrajComer2d2d.H
TrajComer2d2d2d.H
TrajComerLog.H
TrajCostComputer.H
TrajCostDesc.H
TrajFilter.H
TrajFoxFunction.H
TrajFracSmolCrank.H
TrajFracSmolCrankFaster.H
TrajReflect.H
TrajReflect2d.H
TrajSmolCrank.H
TrajSmolCrank1.H
TrajSmolCrankBias.H
TrialMove.H
brownTown2dPassage.C
ccgCost.C
cubicIntegrate.C
diffusionFusion.C
doCrank.C
doCrankDirichlet.C
doFracCrankDirichlet.C
doHarmonicDiffusion.C
doSmoluchowski.C
doSmoluchowskiReflect.C
doTimeFrac.C
doTimeFracCrank.C
dxToArray2d.C
dxToGnuplot2d.C
insertDataDx2d1.C
mapField.C
testFox1.C
useful.H

README.md

DiffusionFusion

This is a program for calculating position-dependent diffusivity functions from trajectory data. It was written by Jeff Comer . The approach is described in:

Comer, Chipot and Gonzalez-Nilo (2013) J. Chem. Theory Comput., 9(2) 876-882, DOI: 10.1021/ct300867e

See the following for information on two-dimensional calculations and using reflecting boundary conditions, which are useful for an orientation angle:

Comer J, Schulten K, Chipot C (2014) Diffusive models of membrane permeation with explicit orientational freedom. J Chem Theory Comput 10(7):2710–2718. doi: 10.1021/ct500209j

See the following for information on use of the Smoluchowski and fractional Smoluchowski solver:

Chipot C, Comer J (2016) Subdiffusion in membrane permeation of small molecules. Sci. Rep. 6:35913. doi: 10.1038/srep35913

Installation

You need the Gnu Scientific Library development package installed (for random numbers). Here is the Ubuntu package, which may or may not help you:

sudo apt-get install gsl-bin libgsl0-dev

You may also have to install OpenMP support for g++ (multithreading). Here is the Ubuntu package, which may or may not help you:

sudo apt-get install libgomp

Then try:

make

On a Mac, this might work better:

make mac

Just running diffusion fusion with no parameters will give you the usage information.

./diffusionFusion

See the Examples/ directory for more information.