Genetic Algorithms for Reflectometry
GArefl is a genetic algorithms reflectivity fitting program based on an early version of the DANSE reflectometry modeling library. It allows simultaneous fitting of X-ray and neutron datasets with arbitrary constraints between the parameters. Users have created models for complex patterns of magnetism spanning multiple layers, and have used it to fit biological samples with volume fractions in solvated proteins.
GArefl is a console based program with models defined in C and plots created using gnuplot. The learning curve is steep, the resulting program allows great flexibility in the choice of fitting paramters, including parameters which are not directly part of the model. This flexibility will be incorporated into the graphical user interface KsRefl, but until then GArefl is the primary software for reflectometry modeling in the DANSE project.
Authors: Paul Kienzle, Mathieu Doucet, Duncan McGillavary.
- Install packages for gnuplot and gfortran. Development tools (gcc, glibc-dev, make, etc.) are probably already installed.
- Install cygwin, being sure to select the development packages for make, gcc and gfortran. The tar and gzip packages should be installed by default. If not you can rerun cygse. You can also install the cygwin gnuplot, though this version will pull in the X11 display server. Pure windows versions of gnuplot are also available, but you will need to modify the gaplot script to include the full installation path.
- Mac OS X
- Install the developer sdk from the install CDs if you have not already done so. Gnuplot and aquaterm binaries are readily available on the net. Fortran binaries are available from the R for OS X page.
- Support incoherent sums of multiple models to one data set.
- Support unpolarized measurements on magnetic samples.
- Suppress logging when not GA running continuously.
- Save parameters in [0-1] or as fitted values.
- BUG: spin-flip cross-sections now fitted properly with L-M.
- Minor release: move source to the DANSE repository and branch it from the DANSE reflectometry main source tree.