niels-bohr-institute-xns-structbiophys / bayesapp

Source code for the BayesApp software package

GitHub repo moved

new GitHub repository: https://github.com/ehb54/GenApp-BayesApp
this repo will not be updated

BayesApp

Source code for the BayesApp software package

online application at GenApp: https://somo.chem.utk.edu/bayesapp/

Calculates the pair distance distribution function, p(r), from a SAXS/SANS dataset by a Bayesian indirect Fourier transformation (BIFT) algorithm

Written by: Steen Hansen
With contributions from: Andreas Haahr Larsen, Martin Cramer Pedersen

File overview

bift.f

source code (fortran)

.github/workflows

instructions for compilation on different OS.

Instructions for running the program

1. Compilation (linux): gfortran -march=native -O3 bift.f -o bift
   -march=native may be left out
   -m64 or -m32 may be added
   it may be necessary to include the "-static" flag
   ... depending on system

2. Run: bift < inputfile.d

3. The file: inputfile.d has to contain the 16 lines:
   input format
   line 1: the name of the data file - compulsory - [string]
   line 2: q_min or a blank line [float]
   line 3: q_max or a blank line [float]
   line 4: nrebin or a blank line [integer]
   line 5: d_max or a blank line [float]*
   line 6: eta (non-dilute solutions) or a blank line [float]**
   line 7: alpha or a blank line [float]*
   line 8: smearing constant or a blank line [float]
   line 9: ratio (non-dilute solutions) or a blank line [float]**
   line 10: method (non-dilute solutions) or a blank line [N]one or [M]oment or [E]vidence**
   line 11: number of points in p(r) or a blank line [integer]
   line 12: number of extra cal or a blank line [integer]
   line 13: transformation or a blank line [D]ebye (default) or [N]egative or [M]axEnt
   line 14: fit constant background or a blank line [Y]es or [N]o
   line 15: non-const rescaling or a blank line [N]on-constant or [C]onstant
   line 16: min points per Shannon bin or a blank line [integer]

* use prefix "f" to Fix value, i.e. f22.0 instead of 22.0 for d_max
if no prefix is given, the input value is used as initial value in the optimization search

** This part of the code (p(r) for non-dilute scatterers) is not maintained and therefore not part of the GUI. There is no garantee that it is working, so use this option with care and be extra critical when interpreting the results. None: fit only alpha and dmax, Moment: fit alpha, d_max and eta, Evidence: fit alpha, dmax, eta and ratio

NB NB The input values are the same as at the web site
Only the first line has to be a non blank line
For further information see the website
The program was tested with gfortran 4.4 and it may
be necessary to include the "-static" flag.

bayesapp's Issues

License information missing

Hello everyone,
that is a great program and I wondered under which conditions it might be possible to include this program in other (open source) software packages for small-angle scattering analysis and under which conditions changes/contributions can be made?
Some licensing information would be very helpful for communicating those conditions. GitHub offers a guide and some templates for very common software licenses:
https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-license-to-a-repository

Thank you very much and best regards!