release-notes/2020/major/deprecated-functionality.rst
release-notes/2020/major/portability.rst
release-notes/2020/major/miscellaneous.rst
+ release-notes/2019/2019.6.rst
release-notes/2019/2019.5.rst
release-notes/2019/2019.4.rst
release-notes/2019/2019.3.rst
GROMACS 2019.5 release notes
----------------------------
-This version was released on TODO, 2019. These release notes
+This version was released on December 23rd, 2019. These release notes
document the changes that have taken place in GROMACS since the
previous 2019.4 version, to fix known issues. It also incorporates all
-fixes made in version 2018.7 and earlier, which you can find described
+fixes made in version 2018.8 and earlier, which you can find described
in the :ref:`release-notes`.
.. Note to developers!
Fixes for ``gmx`` tools
^^^^^^^^^^^^^^^^^^^^^^^
+Make histogram output clearer
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Output gave number of events included in histogram bar as *a.u.*,
+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`
+
+
+Remove problematic output of gmx angle tool
+"""""""""""""""""""""""""""""""""""""""""""
+
+It could happen that the calculation of the standard deviation
+for angles caused a divide by zero error for empty populations.
+Because this standard deviation was meaningless, it has been
+removed.
+
+:issue:`3206`
+
Fixes that affect portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Check that libhwloc headers and runtime match
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+It could happen that the libhwloc headers and library detection would
+lead to a mismatch at compile or runtime that could cause cryptic
+crashes while using mdrun.
+
+:issue:`3200`
+
Miscellaneous
^^^^^^^^^^^^^
:issue:`3176`
Fix duplicate PDB CONECT record output
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+""""""""""""""""""""""""""""""""""""""
PDB "CONECT" record output was duplicated in some instances. Since |Gromacs| does
not use these anywhere, analysis was not affected. The behavior is now fixed.
:issue:`3206`
+Fix performance issue with bonded interactions in wrong GPU stream
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This could lead to a significant loss in performance.
+
+:issue:`3241`
--- /dev/null
+GROMACS 2019.6 release notes
+----------------------------
+
+This version was released on TODO, 2020. These release notes
+document the changes that have taken place in GROMACS since the
+previous 2019.5 version, to fix known issues. It also incorporates all
+fixes made in version 2018.8 and earlier, which you can find described
+in the :ref:`release-notes`.
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on redmine, without the
+ a space between the colon and number!
+
+Fixes where mdrun could behave incorrectly
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixes for ``gmx`` tools
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixes that affect portability
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+Miscellaneous
+^^^^^^^^^^^^^
+
.. toctree::
:maxdepth: 1
+ 2019/2019.6
2019/2019.5
2019/2019.4
2019/2019.3
{
int n, ai, aj;
- std::string form2 = "%%*s";
- std::string format = form2 + "%%d";
+ std::string form2 = "%*s";
+ std::string format = form2 + "%d";
if (sscanf(line, format.c_str(), &ai) == 1)
{
do
{
form2 += "%*s";
- format = form2 + "%%d";
+ format = form2 + "%d";
n = sscanf(line, format.c_str(), &aj);
if (n == 1)
{
#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++)
{
+ 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,
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
}
}
- fp = xvgropen(fn, "RMS Distribution", "RMS (nm)", "a.u.", oenv);
+ fp = xvgropen(fn, "RMS Distribution", "RMS (nm)", "counts", oenv);
for (i = 0; (i < 101); i++)
{
fprintf(fp, "%10g %10d\n", i / fac, histo[i]);
#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"
gmx_bool bAver, bRb, bPeriodic, 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*/
for (first = 0; (first < maxangstat - 1) && (angstat[first + 1] == 0); first++) {}
for (last = maxangstat - 1; (last > 0) && (angstat[last - 1] == 0); last--) {}
- aver = aver2 = 0;
- for (i = 0; (i < nframes); i++)
- {
- aver += RAD2DEG * aver_angle[i];
- aver2 += gmx::square(RAD2DEG * aver_angle[i]);
+ double aver = 0;
+ printf("Found points in the range from %d to %d (max %d)\n", first, last, maxangstat);
+ 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;
+ }
+ }
+ }
+ 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;
+ }
}
aver /= nframes;
- aver2 /= nframes;
- aversig = std::sqrt(aver2 - gmx::square(aver));
- printf("Found points in the range from %d to %d (max %d)\n", first, last, maxangstat);
- printf(" < angle > = %g\n", aver);
- printf("< angle^2 > = %g\n", aver2);
- printf("Std. Dev. = %g\n", aversig);
+ double aversig = correctRadianAngleRange(aver);
+ aversig *= RAD2DEG;
+ aver *= RAD2DEG;
+ printf(" < angle > = %g\n", aversig);
if (mult == 3)
{
if (useGpuForBonded)
{
- auto stream = DOMAINDECOMP(cr)
+ auto stream = havePPDomainDecomposition(cr)
? Nbnxm::gpu_get_command_stream(
fr->nbv->gpu_nbv, gmx::InteractionLocality::NonLocal)
: Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv,
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff