Fix originally contributed by Boris Timofeev.
Fixes #3225
Change-Id: I4862679e4aeae514736df53f0eff44bf3b85f928
which was not clear for users.
+Fix dihedral angle calculation near 180 degree boundary
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The analysis tools could incorrectly calculate properties of torsion angles and their averages
+when close to the -180 or 180 degree boundary.
+
+:issue:`3225`
+
+
Fixes that affect portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/angle_correction.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/listed-forces/bonded.h"
#include "gromacs/math/functions.h"
t_trxstatus *status;
int i, angind, total, teller;
int nangles, n_alloc;
- real t, fraction, pifac, aa, angle;
+ real t, fraction, pifac, angle;
real *angles[2];
matrix box;
rvec *x;
}
/* Average angles */
- aa = 0;
+ double aa = 0;
for (i = 0; (i < nangles); i++)
{
- aa = aa+angles[cur][i];
+ if (!bAngles && i > 0)
+ {
+ real diffa = angles[cur][i] - angles[cur][i-1];
+ diffa = correctRadianAngleRange(diffa);
+ angles[cur][i] = angles[cur][i-1] + diffa;
+ }
+
+ aa = aa + angles[cur][i];
/* angle in rad / 2Pi * max determines bin. bins go from 0 to maxangstat,
even though scale goes from -pi to pi (dihedral) or -pi/2 to pi/2
angle = angles[cur][i];
if (!bAngles)
{
- while (angle < -M_PI)
- {
- angle += 2*M_PI;
- }
- while (angle >= M_PI)
- {
- angle -= 2*M_PI;
- }
-
+ angle = correctRadianAngleRange(angle);
angle += M_PI;
}
}
/* average over all angles */
- (*aver_angle)[teller] = (aa/nangles);
+ aa = correctRadianAngleRange(aa/nangles);
+ (*aver_angle)[teller] = (aa);
/* this copies all current dih. angles to dih[i], teller is frame */
if (bSaveAll)
{
for (i = 0; i < nangles; i++)
{
- dih[i][teller] = angles[cur][i];
+ if (!bAngles)
+ {
+ dih[i][teller] = correctRadianAngleRange(angles[cur][i]);
+ }
+ else
+ {
+ dih[i][teller] = angles[cur][i];
+ }
}
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "angle_correction.h"
+
+#include <algorithm>
+
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+
+real correctRadianAngleRange(const real angle)
+{
+ real correctedAngle = angle;
+ while (correctedAngle < -M_PI)
+ {
+ correctedAngle += 2*M_PI;
+ }
+ while (correctedAngle >= M_PI)
+ {
+ correctedAngle -= 2*M_PI;
+ }
+ return correctedAngle;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_GMXANA_ANGLE_CORRECTION_H
+#define GMX_GMXANA_ANGLE_CORRECTION_H
+
+#include "gromacs/math/units.h"
+
+/*! \brief
+ * Return the angle in radians after correcting to be within range of -PI < \p angle < PI.
+ *
+ * \param[in] angle The angle in radians.
+ * \returns Angle within range.
+ */
+real correctRadianAngleRange(real angle);
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/angle_correction.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/functions.h"
bFrac, /* calculate fraction too? */
bTrans, /* worry about transtions too? */
bCorr; /* correlation function ? */
- real aver, aver2, aversig; /* fraction trans dihedrals */
double tfrac = 0;
char title[256];
real **dih = nullptr; /* mega array with all dih. angles at all times*/
;
}
- aver = aver2 = 0;
- for (i = 0; (i < nframes); i++)
- {
- aver += RAD2DEG*aver_angle[i];
- aver2 += gmx::square(RAD2DEG*aver_angle[i]);
- }
- aver /= nframes;
- aver2 /= nframes;
- aversig = std::sqrt(aver2-gmx::square(aver));
+ double aver = 0;
+ double aver2 = 0;
printf("Found points in the range from %d to %d (max %d)\n",
first, last, maxangstat);
- printf(" < angle > = %g\n", aver);
+ if (bTrans || bCorr || bALL || opt2bSet("-or", NFILE, fnm))
+ { /* It's better to re-calculate Std. Dev per sample */
+ real b_aver = aver_angle[0];
+ real b = dih[0][0];
+ real delta;
+ for (int i = 0; (i < nframes); i++)
+ {
+ delta = correctRadianAngleRange(aver_angle[i] - b_aver);
+ b_aver += delta;
+ aver += b_aver;
+ for (int j = 0; (j < nangles); j++)
+ {
+ delta = correctRadianAngleRange(dih[j][i] - b);
+ b += delta;
+ aver2 += gmx::square(b);
+ }
+ }
+ aver2 /= nangles;
+ }
+ else
+ { /* Incorrect for Std. Dev. */
+ real delta, b_aver = aver_angle[0];
+ for (i = 0; (i < nframes); i++)
+ {
+ delta = correctRadianAngleRange(aver_angle[i] - b_aver);
+ b_aver += delta;
+ aver += b_aver;
+ aver2 += gmx::square(b_aver);
+ }
+ }
+ aver /= nframes;
+ aver2 /= nframes/(RAD2DEG * RAD2DEG);
+ double aversig = correctRadianAngleRange(aver);
+ aversig *= RAD2DEG;
+ aver *= RAD2DEG;
+ printf(" < angle > = %g\n", aversig);
printf("< angle^2 > = %g\n", aver2);
- printf("Std. Dev. = %g\n", aversig);
+ if ((aversig = aver2-gmx::square(aver)) > 0)
+ {
+ printf("Std. Dev. = %g\n", std::sqrt(aversig));
+ }
+ else
+ {
+ printf("Std. Dev. - can't be calculated\n");
+ }
if (mult == 3)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff