- Change parameters in initParams.m
- To run a simulation, run run_bindobs()
- Outputs go to runfiles
- To analyze runs (calculate msd), analyze_bindobs(n) -n: # of files you want to analyze -Outputs go to msdfiles (Note, you can combine steps 2) and 3) by running run_analyze_bindobs()
- To average over grids, averageMSDgrids( ffo, bind, bDiff, sizeObs, parentpath, nameID, bindDirFlag )
-put all the runs you want to average in the same dir,
Figure out what filling fractions, binding energies, size, bound diffusion
you want to average over.
-Say it's just ff = 0.1, be = 0, size = 1, bD = 0.
-If they are all in ./msdfiles, you'd run
averageMSDgrids( 0.1, 0, 0, 1, 'msdfiles/', 'test', 0 )
-If you put them in ./msdfiles/bind00, >> averageMSDgrids( 0.1, 0, 0, 1, 'msdfiles/', 'test', 1 ) -outputs go into gridAveMSDdata/ 5) To calculate Diffusion coefficients, etc, run -[masterD, asymInfo] = getDfromGridAveAsymp( path2files, fileId, ... numBins, threshold, plotFlag, saveFigFlag, verbose ) -Currently uses getHorzAsymptotes which was not what was used in the paper (findHorztlAsymp was)
collectjobs.sh: Goes to run directory, collects all finshed run jobs, and put them in working directory.
submitanalysis.m: Calls SetUpAnalysisMaster which takes all files in ./runfiles, and puts them in run directories in the run directory. Next, it submits analysis_bindobs jobs for them.
SetUpAnalysisMaster: sets up run directories for analysis. It takes all files in ./runfiles, and puts them in run directories in the run directory. It calls initAnalyzeParams where you can edit the run directory path, number of files in a directory, and a trial indicator for identify the job.