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BUMPS(1) | python-bumps man page | BUMPS(1) |

# NAME¶

bumps - data fitting and Bayesian uncertainty modeling for inverse problems

# SYNOPSIS¶

**bumps** [*options*] *modelfile*
[*modelargs*]

**bumps**
[{**-?** | **-h** | **--help**}]

# DESCRIPTION¶

This manual page documents briefly the **bumps** command (
**bumps3** for python3).

This manual page was written for the Debian distribution because
the original program does not have a manual page. Instead, it has
documentation in HTML and in the GNU **info**(1) format; see below.

**bumps** provides a set of routines for curve fitting and
uncertainty analysis from a Bayesian perspective. In addition to traditional
optimizers which search for the best minimum they can find in the search
space, bumps provides uncertainty analysis which explores all viable minima
and finds confidence intervals on the parameters based on uncertainty in the
measured values. Bumps has been used for systems of up to 100 parameters
with tight constraints on the parameters. Full uncertainty analysis requires
hundreds of thousands of function evaluations, which is only feasible for
cheap functions, systems with many processors, or lots of patience.

Bumps includes several traditional local optimizers such as Nelder-Mead simplex, BFGS and differential evolution. Bumps uncertainty analysis uses Markov chain Monte Carlo to explore the parameter space. Although it was created for curve fitting problems, Bumps can explore any probability density function, such as those defined by PyMC. In particular, the bumps uncertainty analysis works well with correlated parameters.

The modelfile is a Python script (i.e., a series of Python commands) which sets up the data, the models, and the fittable parameters. The model arguments are available in the modelfile as sys.argv[1:]. Model arguments may not start with '-'.

# OPTIONS¶

The program follows the usual GNU command line syntax, with long
options starting with two dashes (`-'). A summary of options is included
below. For a complete description, see the HTML documentation or
**info**(1) files.

**--preview**

**--pars=filename**

*modelname*.par

**--plot=log [linear|log|residuals]**

**--simulate**

**--simrandom**

**--shake**

**--noise=5%**

**--seed=integer**

**--err**

**--cov**

**--entropy**

**--staj**

**--edit**

**--view=linear|log**

**--store=path**

**--overwrite**

**--resume=path [dream]**

**--parallel**

**--mpi**

**--batch**

**--noshow**

**--remote**

**--notify=user@email**

**--queue=http://reflectometry.org**

**--time=inf**

**--fit=amoeba
[amoeba|de|dream|lm|newton|ps|pt|rl|snobfit]**

**--steps=400
[amoeba|de|dream|lm|newton|ps|pt|rl|snobfit]**

**--samples=1e4 [dream]**

**--xtol=1e-4 [de, amoeba]**

**--ftol=1e-4 [de, amoeba]**

**--pop=10 [dream, de, rl, ps]**

**--burn=100 [dream, pt]**

**--thin=1 [dream]**

**--nT=25**

**--Tmin=0.1**

**--Tmax=10 [pt]**

**--CR=0.9 [de, rl, pt]**

**--starts=1 [newton, rl, amoeba]**

**--keep_best**

**--init=eps [dream]**

eps

lhs

cov

random

**--stepmon**

**--resynth=0**

**--time_model**

**--profile**

**--chisq**

**-m**, **-c**, **-p command**

m

c

p

**-i**

**-?**, **-h**, **--help**

# SEE ALSO¶

Bumps is documented fully in HTML at
**/usr/share/doc/python-bumps-doc/html/index.html**[1] and also in the
**info**(1) system.

# AUTHOR¶

**Drew Parsons** <dparsons@debian.org>

# COPYRIGHT¶

Copyright © 2017 Drew Parsons

This manual page was written for the Debian system (and may be used by others).

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at your option) any later version published by the Free Software Foundation.

On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

# NOTES¶

- 1.
- /usr/share/doc/python-bumps-doc/html/index.html

10/29/2017 | bumps |