remove unneccessary parameter in bootstrapping function

.gitignore

@@ -1,4 +1,5 @@
 target
 reference
 .idea
-*bench.*
+*bench.*
+*.sublime*

Cargo.lock

@@ -1,372 +1,397 @@
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Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "wham"
-version = "0.9.3"
-authors = ["D. Bauer <bauer@bio.tu-darmstadt.de>"]
+version = "0.9.8"
+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"
@@ -13,6 +13,9 @@ rand = "0.5.5"
 GSL = "1.0.0"
 rayon = "1.0.3"
 
+[dev-dependencies]
+assert_approx_eq = "1.1.0"
+
 [profile.release]
 opt-level = 2
 

README.md

@@ -1,4 +1,4 @@
-[![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.1488598.svg)](https://doi.org/10.5281/zenodo.1488598)
+[![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)
 
 
 
@@ -81,19 +81,20 @@ one can estimate the error as standard deviation between the N bootstrapping run
 Autocorrelation Estimates, JCTC, 6(12), 3713-3720*.
 
 To perform bayesian bootstrapping in WHAM, use the ```-bt <RUNS>``` flag to perform <RUNS> individual bootstrapping
-runs. The error estimates of bin probabilities and free energy will be given as separate column (+/-) in the output file.
-If no error analysis is performed, these columns are set to 0.0.
+runs. The error estimates of bin probabilities and free energy will be given as standard error (SE) in a 
+separate column (+/-) in the output file. If no error analysis is performed, these columns are set to 0.0.
 
 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
 ---
+- better error estimation
 - Autocorrelation
 - Replica exchange
 

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
--0.408200    30.366556    0.000000    0.000000    0.000000
--0.345400    31.615252    0.000000    0.000000    0.000000
--0.282600    32.781716    0.000000    0.000000    0.000000
--0.219800    33.731378    0.000000    0.000000    0.000000
--0.157000    34.476014    0.000000    0.000000    0.000000
--0.094200    35.387300    0.000000    0.000000    0.000000
--0.031400    35.579756    0.000000    0.000000    0.000000
-0.031400    35.520194    0.000000    0.000000    0.000000
-0.094200    35.344763    0.000000    0.000000    0.000000
-0.157000    34.886460    0.000000    0.000000    0.000000
-0.219800    33.633998    0.000000    0.000000    0.000000
-0.282600    32.686511    0.000000    0.000000    0.000000
-0.345400    31.211777    0.000000    0.000000    0.000000
-0.408200    29.680451    0.000000    0.000000    0.000000
-0.471000    28.032242    0.000000    0.000001    0.000000
-0.533800    26.439599    0.000000    0.000002    0.000000
-0.596600    24.432467    0.000000    0.000003    0.000000
-0.659400    22.309893    0.000000    0.000008    0.000000
-0.722200    20.186040    0.000000    0.000019    0.000000
-0.785000    18.295046    0.000000    0.000040    0.000000
-0.847800    16.221232    0.000000    0.000093    0.000000
-0.910600    14.251911    0.000000    0.000204    0.000000
-0.973400    12.562353    0.000000    0.000402    0.000000
-1.036200    11.184029    0.000000    0.000698    0.000000
-1.099000    10.040677    0.000000    0.001103    0.000000
-1.161800    9.369064    0.000000    0.001444    0.000000
-1.224600    9.095392    0.000000    0.001612    0.000000
-1.287400    9.256035    0.000000    0.001511    0.000000
-1.350200    9.814068    0.000000    0.001208    0.000000
-1.413000    10.945207    0.000000    0.000768    0.000000
-1.475800    12.518898    0.000000    0.000409    0.000000
-1.538600    14.409744    0.000000    0.000191    0.000000
-1.601400    16.451965    0.000000    0.000084    0.000000
-1.664200    18.589166    0.000000    0.000036    0.000000
-1.727000    20.669504    0.000000    0.000016    0.000000
-1.789800    22.804791    0.000000    0.000007    0.000000
-1.852600    24.531690    0.000000    0.000003    0.000000
-1.915400    26.182612    0.000000    0.000002    0.000000
-1.978200    27.279439    0.000000    0.000001    0.000000
-2.041000    28.571380    0.000000    0.000001    0.000000
-2.103800    29.328969    0.000000    0.000000    0.000000
-2.166600    29.897739    0.000000    0.000000    0.000000
-2.229400    30.320908    0.000000    0.000000    0.000000
-2.292200    30.065391    0.000000    0.000000    0.000000
-2.355000    29.809137    0.000000    0.000000    0.000000
-2.417800    29.340601    0.000000    0.000000    0.000000
-2.480600    28.473346    0.000000    0.000001    0.000000
-2.543400    27.679353    0.000000    0.000001    0.000000
-2.606200    26.453160    0.000000    0.000002    0.000000
-2.669000    24.424649    0.000000    0.000003    0.000000
-2.731800    22.285933    0.000000    0.000008    0.000000
-2.794600    19.958407    0.000000    0.000021    0.000000
-2.857400    17.606291    0.000000    0.000053    0.000000
-2.920200    15.420138    0.000000    0.000128    0.000000
-2.983000    13.069599    0.000000    0.000328    0.000000
-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    0.069244    0.003494    0.000067
+-3.047345    5.365727    0.068503    0.007168    0.000135
+-2.984513    3.873190    0.065883    0.013039    0.000226
+-2.921681    2.953162    0.066856    0.018855    0.000334
+-2.858849    1.949554    0.066705    0.028195    0.000501
+-2.796017    1.391747    0.064012    0.035261    0.000576
+-2.733186    1.128270    0.061522    0.039189    0.000598
+-2.670354    0.839970    0.060810    0.043991    0.000653
+-2.607522    0.624769    0.061888    0.047955    0.000733
+-2.544690    0.663757    0.062566    0.047211    0.000736
+-2.481858    1.051932    0.061093    0.040407    0.000616
+-2.419026    1.463048    0.062547    0.034267    0.000543
+-2.356194    1.990616    0.057022    0.027734    0.000373
+-2.293363    2.190692    0.044029    0.025597    0.000202
+-2.230531    2.553036    0.041867    0.022136    0.000157
+-2.167699    2.572522    0.044817    0.021964    0.000184
+-2.104867    2.472360    0.038778    0.022863    0.000155
+-2.042035    2.517562    0.030296    0.022453    0.000150
+-1.979203    2.469778    0.025852    0.022887    0.000167
+-1.916372    2.223125    0.030799    0.025266    0.000411
+-1.853540    2.080157    0.024928    0.026756    0.000365
+-1.790708    1.793841    0.027529    0.030011    0.000475
+-1.727876    1.458784    0.026130    0.034326    0.000462
+-1.665044    0.914441    0.024774    0.042697    0.000576
+-1.602212    0.303813    0.020400    0.054540    0.000701
+-1.539380    0.268335    0.020423    0.055321    0.000733
+-1.476549    0.000000    0.020271    0.061604    0.000835
+-1.413717    0.537061    0.023895    0.049671    0.000735
+-1.350885    1.439940    0.023678    0.034586    0.000528
+-1.288053    2.391838    0.025951    0.023614    0.000386
+-1.225221    3.779470    0.026215    0.013538    0.000224
+-1.162389    5.685555    0.028543    0.006305    0.000109
+-1.099557    7.661896    0.030579    0.002855    0.000051
+-1.036726    9.946594    0.039243    0.001142    0.000022
+-0.973894    12.359408    0.054067    0.000434    0.000009
+-0.911062    14.954655    0.066597    0.000153    0.000004
+-0.848230    17.742242    0.073582    0.000050    0.000002
+-0.785398    20.555785    0.074644    0.000016    0.000001
+-0.722566    22.811160    0.078503    0.000007    0.000000
+-0.659734    25.178094    0.088961    0.000003    0.000000
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