Fixed the output format of g_principal

Gromacs-4.6 and earlier versions had the output transposed. This
patch fixes it such that paxisN.dat contains the x/y/z components
of the N:th prinicipal axis. The default file output names have
been changed to paxisN.dat to increase the probability that users
who rely on old scripts will need to read the help text and find
the changed format.

Fixes #1441, related to #609.

Change-Id: Ic1ed9370145d3389ae8f43c2a419765dabf3a66f

diff --git a/src/gromacs/gmxana/gmx_principal.c b/src/gromacs/gmxana/gmx_principal.c
index daa2425c231d8ddea331bf33dcb93994e8b6ba10..9b82d19eb0a493366ac8c71d9858199be21dfbc9 100644 (file)
--- a/src/gromacs/gmxana/gmx_principal.c
+++ b/src/gromacs/gmxana/gmx_principal.c
@@ -79,7 +79,11 @@ int gmx_principal(int argc, char *argv[])
 {
     const char     *desc[] = {
         "[THISMODULE] calculates the three principal axes of inertia for a group",
-        "of atoms.",
+        "of atoms. NOTE: Old versions of Gromacs wrote the output data in a",
+        "strange transposed way. As of Gromacs-5.0, the output file paxis1.dat",
+        "contains the x/y/z components of the first (major) principal axis for",
+        "each frame, and similarly for the middle and minor axes in paxis2.dat",
+        "and paxis3.dat."
     };
     static gmx_bool foo = FALSE;
 
@@ -110,9 +114,9 @@ int gmx_principal(int argc, char *argv[])
         { efTRX, "-f",   NULL,       ffREAD },
         { efTPS, NULL,   NULL,       ffREAD },
         { efNDX, NULL,   NULL,       ffOPTRD },
-        { efDAT, "-a1",  "axis1",    ffWRITE },
-        { efDAT, "-a2",  "axis2",    ffWRITE },
-        { efDAT, "-a3",  "axis3",    ffWRITE },
+        { efDAT, "-a1",  "paxis1",   ffWRITE },
+        { efDAT, "-a2",  "paxis2",   ffWRITE },
+        { efDAT, "-a3",  "paxis3",   ffWRITE },
         { efDAT, "-om",  "moi",      ffWRITE }
     };
 #define NFILE asize(fnm)
@@ -143,9 +147,9 @@ int gmx_principal(int argc, char *argv[])
 
         calc_principal_axes(&top, x, index, gnx, axes, moi);
 
-        fprintf(axis1, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[XX][XX], axes[YY][XX], axes[ZZ][XX]);
-        fprintf(axis2, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[XX][YY], axes[YY][YY], axes[ZZ][YY]);
-        fprintf(axis3, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[XX][ZZ], axes[YY][ZZ], axes[ZZ][ZZ]);
+        fprintf(axis1, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[XX][XX], axes[XX][YY], axes[XX][ZZ]);
+        fprintf(axis2, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
+        fprintf(axis3, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY], axes[ZZ][ZZ]);
         fprintf(fmoi,  "%15.10f     %15.10f  %15.10f  %15.10f\n", t, moi[XX], moi[YY], moi[ZZ]);
     }
     while (read_next_x(oenv, status, &t, x, box));