Corrected documentation about eigenvalue handling

Some file format docs were out of step with the implementation in
eigio.cpp.

The behaviour of gmx anaeig -eig -eig2 was not properly documented.

Change-Id: I55c4a0ab640f026e6e8a424203d54379e634a5b6

diff --git a/src/gromacs/gmxana/gmx_anaeig.cpp b/src/gromacs/gmxana/gmx_anaeig.cpp
index 15fbfb13f403129bd9c1959b6a8406e4009f6c8f..702d6f208e5e43b3bf7b2b2cce1bdaea97b9306d 100644 (file)
--- a/src/gromacs/gmxana/gmx_anaeig.cpp
+++ b/src/gromacs/gmxana/gmx_anaeig.cpp
@@ -1024,9 +1024,11 @@ int gmx_anaeig(int argc, char *argv[])
         "of both files will be used unless [TT]-first[tt] and [TT]-last[tt]",
         "have been set explicitly.[PAR]",
 
-        "When [TT]-v[tt], [TT]-eig[tt], [TT]-v2[tt] and [TT]-eig2[tt] are given,",
-        "a single number for the overlap between the covariance matrices is",
-        "generated. The formulas are::",
+        "When [TT]-v[tt] and [TT]-v2[tt] are given, a single number for the",
+        "overlap between the covariance matrices is generated. Note that the",
+        "eigenvalues are by default read from the timestamp field in the",
+        "eigenvector input files, but when [TT]-eig[tt], or [TT]-eig2[tt] are",
+        "given, the corresponding eigenvalues are used instead. The formulas are::",
         "",
         "         difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))",
         " normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))",

diff --git a/src/gromacs/gmxana/gmx_covar.cpp b/src/gromacs/gmxana/gmx_covar.cpp
index b7ee514a5697bfc952d34f2463949ae537b7e774..34a5e03c3119ed662aa41752d7416979b1f0cd00 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.cpp
+++ b/src/gromacs/gmxana/gmx_covar.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -75,7 +75,8 @@ int gmx_covar(int argc, char *argv[])
         "the reference structure for the fit is written first with t=-1.",
         "The average (or reference when [TT]-ref[tt] is used) structure is",
         "written with t=0, the eigenvectors",
-        "are written as frames with the eigenvector number as timestamp.",
+        "are written as frames with the eigenvector number and eigenvalue",
+        "as step number and timestamp, respectively.",
         "[PAR]",
         "The eigenvectors can be analyzed with [gmx-anaeig].",
         "[PAR]",

diff --git a/src/gromacs/gmxana/gmx_nmeig.cpp b/src/gromacs/gmxana/gmx_nmeig.cpp
index 0c363ed7c11c0c5c44c79a032e6fe3cd9b991ede..531c004308585b3300d9337fc5608c0b9a972aa0 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmeig.cpp
+++ b/src/gromacs/gmxana/gmx_nmeig.cpp
@@ -302,7 +302,8 @@ int gmx_nmeig(int argc, char *argv[])
         "which can be calculated with [gmx-mdrun].",
         "The eigenvectors are written to a trajectory file ([TT]-v[tt]).",
         "The structure is written first with t=0. The eigenvectors",
-        "are written as frames with the eigenvector number as timestamp.",
+        "are written as frames with the eigenvector number and eigenvalue",
+        "written as step number and timestamp, respectively.",
         "The eigenvectors can be analyzed with [gmx-anaeig].",
         "An ensemble of structures can be generated from the eigenvectors with",
         "[gmx-nmens]. When mass weighting is used, the generated eigenvectors",