From: Andrey Alekseenko <al42and@gmail.com>
Date: Thu, 1 Jul 2021 10:39:50 +0000 (+0300)
Subject: Make ExpfitTest.EffnERREST well defined
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=f3adc2fabe650b77fccf2a35c36671900c341eb3;p=alexxy%2Fgromacs.git

Make ExpfitTest.EffnERREST well defined

The original test was poorly constructed, and the τ₂ fitting parameter
was not defined for the test data: with α = 1, it could take any value
and the function would fit just the same.

Here, we replace the test data with the one where 0<α<1, and thus both
τ₁ and τ₂ are well-defined.

Also updated the documentation to reflect the actual function used in
the code: it was missing a prefactor of 2.

Closes #3955
---

diff --git a/docs/reference-manual/analysis/curve-fitting.rst b/docs/reference-manual/analysis/curve-fitting.rst
index dafc3eb2e6..e3650f8bd9 100644
--- a/docs/reference-manual/analysis/curve-fitting.rst
+++ b/docs/reference-manual/analysis/curve-fitting.rst
@@ -58,8 +58,8 @@ Under the hood |Gromacs| implements some more fitting functions, namely a
 function to estimate the error in time-correlated data due to Hess \ :ref:`149 <refHess2002a>`:
 
 .. math:: \varepsilon^2(t) =
-          \alpha\tau_1\left(1+\frac{\tau_1}{t}\left(e^{-t/\tau_1}-1\right)\right)
-                + (1-\alpha)\tau_2\left(1+\frac{\tau_2}{t}\left(e^{-t/\tau_2}-1\right)\right)
+          2 \alpha\tau_1\left(1+\frac{\tau_1}{t}\left(e^{-t/\tau_1}-1\right)\right)
+                + 2 (1-\alpha)\tau_2\left(1+\frac{\tau_2}{t}\left(e^{-t/\tau_2}-1\right)\right)
           :label: eqntimecorrerror
 
 where :math:`\tau_1` and :math:`\tau_2` are time constants (with
diff --git a/src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml b/src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml
index 5247edc079..d678c31337 100644
--- a/src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml
+++ b/src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml
@@ -3,8 +3,8 @@
 <ReferenceData>
   <Sequence Name="result">
     <Int Name="Length">3</Int>
-    <Real>0.50082180382778319</Real>
-    <Real>1</Real>
-    <Real>103.32999340041971</Real>
+    <Real>1.2</Real>
+    <Real>0.99</Real>
+    <Real>34.5</Real>
   </Sequence>
 </ReferenceData>
diff --git a/src/gromacs/correlationfunctions/tests/testERREST.xvg b/src/gromacs/correlationfunctions/tests/testERREST.xvg
index 4f28dfc34b..7f794647b4 100644
--- a/src/gromacs/correlationfunctions/tests/testERREST.xvg
+++ b/src/gromacs/correlationfunctions/tests/testERREST.xvg
@@ -1,501 +1,503 @@
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+# import numpy as np; t1, a, t2 = 1.2, 0.99, 34.5; t = np.linspace(1, 8001, 501); e2 = 2*a*t1*(1+t1/t*(np.exp(-t/t1)-1)) + 2*(1-a)*t2*(1+t2/t*(np.exp(-t/t2)-1)); np.savetxt('testERREST.xvg', np.array([t, e2]).T, ('%d', '%.7f'), header=open(__file__).readlines()[0])
+# 
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