Hamiltonian Markov Chain Monte Carlo (HMCMC)
Matlab codes accompaning the paper: Parameter estimation for X-ray scattering analysis with Hamiltonian Markov Chain Monte Carlo, J. Synchrotron Radiat. 29(3) 2022
Installation instructions:
Install Automatic Differentiation toolbox for Matlab (ADiMat), available at https://www.sc.informatik.tu-darmstadt.de/res/sw/adimat/
Requires the Statistics and Machine Learning Toolbox for Matlab
Download multiESS.m, available at https://github.com/lacerbi/multiESS
Example script folders:
- SiOx_SAXS_HMCMC: with Hamiltonian MCMC
Step1_hmcmc_SAXS_run: run HMCMC and save result
Step2_hmcmc_SAXS_result_analysis: load result, analyze and plot
Step3_hmcmc_correlation_analysis: parameter correlation analysis
- SiOx_SAXS_MCMC: with random-walk MCMC intialized from HMCMC
Step1_mcmc_simultanous_SAXS_run
Step2_mcmc_analysis
- LipidBilayer_HMCMC
Step1_xref_lipidbilayer_HMCMC_run
Step2_xref_lipidbilayer_result_analysis
- XWFH_HMCMC: Matlab code and saved result for XWFH
Step_1_hmcmc_XWFH_run: run HMCMC and save result
Step_2_hmcmc_XWFH_result_analysis_and_plot: load result, analyze and generate figures
Use the code at your own risk.