Merge release-4-6 into release-5-0

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_covar.c

diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
index 501597e9acb7addff70ca18cbb79a2a8eb22395d..c9faa784de876a09870107c1decc63a88341790f 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.c
+++ b/src/gromacs/gmxana/gmx_covar.c
@@ -556,7 +556,7 @@ int gmx_covar(int argc, char *argv[])
     out = xvgropen(eigvalfile,
                    "Eigenvalues of the covariance matrix",
                    "Eigenvector index", str, oenv);
-    for (i = 0; (i < ndim); i++)
+    for (i = 0; (i < end); i++)
     {
         fprintf (out, "%10d %g\n", (int)i+1, eigenvalues[ndim-1-i]);
     }
@@ -567,6 +567,9 @@ int gmx_covar(int argc, char *argv[])
         if (nframes-1 < ndim)
         {
             end = nframes-1;
+            fprintf(out, "WARNING: there are fewer frames in your trajectory than there are\n");
+            fprintf(out, "degrees of freedom in your system. Only generating the first\n");
+            fprintf(out, "%d out of %d eigenvectors and eigenvalues.\n", end, (int)ndim);
         }
         else
         {
@@ -641,7 +644,7 @@ int gmx_covar(int argc, char *argv[])
     fprintf(out, "Trace of the covariance matrix after diagonalizing: %g\n\n",
             sum);
 
-    fprintf(out, "Wrote %d eigenvalues to %s\n", (int)ndim, eigvalfile);
+    fprintf(out, "Wrote %d eigenvalues to %s\n", (int)end, eigvalfile);
     if (WriteXref == eWXR_YES)
     {
         fprintf(out, "Wrote reference structure to %s\n", eigvecfile);