From 4d608f1f432c2c1b64a064b18dcf305bc700f45b Mon Sep 17 00:00:00 2001 From: Mark Abraham Date: Wed, 15 Sep 2021 11:29:55 +0200 Subject: [PATCH] Make static selections of large index groups work. The default allocation size is the number of atoms, but this does not work for large static selections. Such selections might well be used with gmx distance for listing more pairs of atoms than there are atoms. Fixed by allocating the needed size. Fixes #4148 --- docs/release-notes/2021/2021.4.rst | 13 + src/gromacs/selection/evaluate.cpp | 3 +- .../trajectoryanalysis/tests/distance.cpp | 18 +- ...ceModuleTest_HandlesSelectionFromGroup.xml | 2094 +++++++++++++++ ...uleTest_HandlesSelectionFromLargeGroup.xml | 2270 +++++++++++++++++ .../trajectoryanalysis/tests/simple.ndx | 37 + 6 files changed, 4433 insertions(+), 2 deletions(-) create mode 100644 src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml create mode 100644 src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml create mode 100644 src/gromacs/trajectoryanalysis/tests/simple.ndx diff --git a/docs/release-notes/2021/2021.4.rst b/docs/release-notes/2021/2021.4.rst index 69a9b7cabe..8d44aea039 100644 --- a/docs/release-notes/2021/2021.4.rst +++ b/docs/release-notes/2021/2021.4.rst @@ -24,6 +24,19 @@ grompp now prints a note again when combining center of mass motion removal and :issue:`4128` +Static selections of large index groups now work +"""""""""""""""""""""""""""""""""""""""""""""""" + +Commands like ``gmx distance -f traj.xtc -n ndx.ndx -select "group +\"Contacts\""`` only worked if the size of ``Contacts`` was less than +the number of atoms. This restriction was a bug, and has been fixed so +that ``Contacts`` make take any size. + +Other similar uses of static selections derived from index groups will +also now work. + +:issue:`4148` + Fixes that affect portability ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp index fd2be14434..a6b511a305 100644 --- a/src/gromacs/selection/evaluate.cpp +++ b/src/gromacs/selection/evaluate.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team. * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team. - * Copyright (c) 2019,2020, by the GROMACS development team, led by + * Copyright (c) 2019,2020,2021, 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. @@ -522,6 +522,7 @@ void _gmx_sel_evaluate_static(gmx_sel_evaluate_t* /* data */, { if (sel->flags & SEL_UNSORTED) { + gmx_ana_index_reserve(sel->v.u.g, sel->u.cgrp.isize); // This only works if g contains all the atoms, but that is currently // the only supported case. gmx_ana_index_copy(sel->v.u.g, &sel->u.cgrp, false); diff --git a/src/gromacs/trajectoryanalysis/tests/distance.cpp b/src/gromacs/trajectoryanalysis/tests/distance.cpp index 49b0f8cb63..95706b6426 100644 --- a/src/gromacs/trajectoryanalysis/tests/distance.cpp +++ b/src/gromacs/trajectoryanalysis/tests/distance.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013,2014,2019, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2019,2021, 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. @@ -90,4 +90,20 @@ TEST_F(DistanceModuleTest, HandlesDynamicSelections) runTest(CommandLine(cmdline)); } +TEST_F(DistanceModuleTest, HandlesSelectionFromGroup) +{ + const char* const cmdline[] = { "distance", "-select", "group \"Contacts\"" }; + setInputFile("-n", "simple.ndx"); + setTopology("simple.gro"); + runTest(CommandLine(cmdline)); +} + +TEST_F(DistanceModuleTest, HandlesSelectionFromLargeGroup) +{ + const char* const cmdline[] = { "distance", "-select", "group \"ManyContacts\"" }; + setInputFile("-n", "simple.ndx"); + setTopology("simple.gro"); + runTest(CommandLine(cmdline)); +} + } // namespace diff --git a/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml new file mode 100644 index 0000000000..73018700e8 --- /dev/null +++ b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml @@ -0,0 +1,2094 @@ + + 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