remove 1d test because of cargo size limit

.gitignore

@@ -1,4 +1,4 @@
 target
 reference
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-bench.sh
+*bench.*

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Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "wham"
-version = "0.9.0"
-authors = ["D. Bauer <bauer@bio.tu-darmstadt.de>"]
+version = "0.9.6"
+authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
 description = "An implementation of the weighted histogram analysis method"
 license = "GPL-3.0"
 repository = "https://github.com/danijoo/WHAM"
@@ -11,9 +11,10 @@ clap = {version="2.32.0", features=['yaml']}
 error-chain = "0.12.0"
 rand = "0.5.5"
 GSL = "1.0.0"
+rayon = "1.0.3"
 
 [profile.release]
 opt-level = 2
 
 [features]
-default = ["GSL/v2"]
+default = ["GSL/v2"]

README.md

@@ -1,4 +1,6 @@
-[![Build Status](https://travis-ci.com/danijoo/WHAM.svg?branch=master)](https://travis-ci.com/danijoo/WHAM) [![crates.io](https://img.shields.io/badge/crates.io-orange.svg?longCache=true)](https://www.crates.io/crates/wham)
+[![Build Status](https://travis-ci.com/danijoo/WHAM.svg?branch=master)](https://travis-ci.com/danijoo/WHAM) [![crates.io](https://img.shields.io/badge/crates.io-orange.svg?longCache=true)](https://www.crates.io/crates/wham) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1488597.svg)](https://doi.org/10.5281/zenodo.1488597)
+
+
 
 Weighted Histogram Analysis Method (WHAM)
 ===
@@ -10,6 +12,7 @@ from umbrella sampling simulations. For more details on the method, I suggest *R
 Features
 ---
 - Fast, especially for small systems
+- Multithreaded
 - Multidimensional
 - Error analysis
 - Unit tested
@@ -85,20 +88,22 @@ Examples
 ---
 The example folder contains input and output files for two simple test systems:
 
-- 1d: Phi torsion angle of dialanine in vaccum
-- 2d: Phi and psi torsion angles of the same system
+- 1d_cyclic: Phi torsion angle of dialanine in vaccum
+- 2d_cyclic: Phi and psi torsion angles of the same system
 
 
 TODO
 ---
-- Multithreading (?)
+- better error estimation
 - Autocorrelation
 - Replica exchange
 
-License 
+License & Citing
 ---
 WHAM is licensed under the GPL-3.0 license. Please read the LICENSE file in this
 repository for more information.
 
+There's no publication for this WHAM implementation. However, there is a citeabe DOI. If you use this software for your work, please consider citing it: *Bauer, D, WHAM - An efficient weighted histogram analysis implementation written in Rust, Zenodo.  https://doi.org/10.5281/zenodo.1488597*
+
 Parts of this work, especially some perfomance optimizations and the I/O format, are inspired by the
 implementation of A. Grossfield (*Grossfield, A, WHAM: the weighted histogram analysis method, http://membrane.urmc.rochester.edu/content/wham*).

example/1d/wham.out

@@ -1,101 +0,0 @@
-#coord1    Free Energy    +/-    Probability    +/-
--3.108600    7.118166    0.000000    0.003561    0.000000
--3.045800    5.331290    0.000000    0.007290    0.000000
--2.983000    3.879241    0.000000    0.013048    0.000000
--2.920200    2.968659    0.000000    0.018796    0.000000
--2.857400    1.942494    0.000000    0.028362    0.000000
--2.794600    1.418408    0.000000    0.034994    0.000000
--2.731800    1.169398    0.000000    0.038668    0.000000
--2.669000    0.843024    0.000000    0.044073    0.000000
--2.606200    0.636021    0.000000    0.047887    0.000000
--2.543400    0.720123    0.000000    0.046299    0.000000
--2.480600    1.066434    0.000000    0.040297    0.000000
--2.417800    1.509855    0.000000    0.033734    0.000000
--2.355000    2.015549    0.000000    0.027544    0.000000
--2.292200    2.226942    0.000000    0.025306    0.000000
--2.229400    2.573176    0.000000    0.022026    0.000000
--2.166600    2.591946    0.000000    0.021861    0.000000
--2.103800    2.476835    0.000000    0.022893    0.000000
--2.041000    2.513953    0.000000    0.022555    0.000000
--1.978200    2.470032    0.000000    0.022956    0.000000
--1.915400    2.227585    0.000000    0.025299    0.000000
--1.852600    2.105310    0.000000    0.026570    0.000000
--1.789800    1.778779    0.000000    0.030286    0.000000
--1.727000    1.447127    0.000000    0.034593    0.000000
--1.664200    0.906384    0.000000    0.042968    0.000000
--1.601400    0.304263    0.000000    0.054699    0.000000
--1.538600    0.247397    0.000000    0.055960    0.000000
--1.475800    0.000000    0.000000    0.061795    0.000000
--1.413000    0.536142    0.000000    0.049843    0.000000
--1.350200    1.428046    0.000000    0.034859    0.000000
--1.287400    2.398149    0.000000    0.023627    0.000000
--1.224600    3.784647    0.000000    0.013552    0.000000
--1.161800    5.696583    0.000000    0.006297    0.000000
--1.099000    7.656158    0.000000    0.002870    0.000000
--1.036200    9.955000    0.000000    0.001142    0.000000
--0.973400    12.357407    0.000000    0.000436    0.000000
--0.910600    14.954254    0.000000    0.000154    0.000000
--0.847800    17.745327    0.000000    0.000050    0.000000
--0.785000    20.559461    0.000000    0.000016    0.000000
--0.722200    22.783560    0.000000    0.000007    0.000000
--0.659400    25.175865    0.000000    0.000003    0.000000
--0.596600    26.419980    0.000000    0.000002    0.000000
--0.533800    27.885999    0.000000    0.000001    0.000000
--0.471000    29.029334    0.000000    0.000001    0.000000
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--0.157000    34.476014    0.000000    0.000000    0.000000
--0.094200    35.387300    0.000000    0.000000    0.000000
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-3.045800    11.036085    0.000000    0.000740    0.000000
-3.108600    9.015657    0.000000    0.001664    0.000000

example/1d_cyclic/README.txt

@@ -0,0 +1,9 @@
+Example data: Dialanine torsion angle at 300K
+wham.out was produced with the folling settings:
+
+wham --max pi --min -pi --cyclic\
+    --bins 100 \
+    -T 300 \
+    -f metadata.dat \
+    -o wham.out \
+    --bt 100 --seed 1234

example/1d_cyclic/wham.out

@@ -0,0 +1,101 @@
+#coord1    Free Energy    +/-    Probability    +/-
+-3.110177    7.158102    0.476037    0.003494    0.000667
+-3.047345    5.365727    0.470738    0.007168    0.001353
+-2.984513    3.873190    0.433120    0.013039    0.002264
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