}
/*! \brief
- * Removes solvent molecules that overlap with the solute, and optionally also
- * those that are outside a given shell radius from the solute.
+ * Remove all solvent molecules outside a give radius from the solute.
*
- * \param[in,out] atoms Solvent atoms.
- * \param[in,out] x Solvent positions.
- * \param[in,out] v Solvent velocities (can be empty).
- * \param[in,out] r Solvent exclusion radii.
- * \param[in] pbc PBC information.
- * \param[in] x_solute Solute positions.
- * \param[in] r_solute Solute exclusion radii.
- * \param[in] rshell If >0, only keep solvent atoms within a shell of
- * this size from the solute.
+ * \param[in,out] atoms Solvent atoms.
+ * \param[in,out] x_solvent Solvent positions.
+ * \param[in,out] v_solvent Solvent velocities.
+ * \param[in,out] r Atomic exclusion radii.
+ * \param[in] pbc PBC information.
+ * \param[in] x_solute Solute positions.
+ * \param[in] rshell The radius outside the solute molecule.
*/
-static void removeSoluteOverlap(t_atoms *atoms, std::vector<RVec> *x,
- std::vector<RVec> *v, std::vector<real> *r,
- const t_pbc &pbc,
- const std::vector<RVec> &x_solute,
- const std::vector<real> &r_solute,
- real rshell)
+static void removeSolventOutsideShell(t_atoms *atoms,
+ std::vector<RVec> *x_solvent,
+ std::vector<RVec> *v_solvent,
+ std::vector<real> *r,
+ const t_pbc &pbc,
+ const std::vector<RVec> &x_solute,
+ real rshell)
{
- const real maxRadius1
- = *std::max_element(r->begin(), r->end());
- const real maxRadius2
- = *std::max_element(r_solute.begin(), r_solute.end());
-
gmx::AtomsRemover remover(*atoms);
- // If rshell is >0, the neighborhood search looks at all pairs
- // within rshell, and unmarks those that are within the cutoff.
- // This line marks everything, so that solvent outside rshell remains
- // marked after the loop.
- // Without rshell, the neighborhood search only marks the overlapping
- // solvent atoms, and all others are left alone.
- if (rshell > 0.0)
+ gmx::AnalysisNeighborhood nb;
+ nb.setCutoff(rshell);
+ gmx::AnalysisNeighborhoodPositions posSolute(x_solute);
+ gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, posSolute);
+ gmx::AnalysisNeighborhoodPositions pos(*x_solvent);
+ gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
+ gmx::AnalysisNeighborhoodPair pair;
+
+ // Remove everything
+ remover.markAll();
+ // Now put back those within the shell without checking for overlap
+ while (pairSearch.findNextPair(&pair))
{
- remover.markAll();
+ remover.markResidue(*atoms, pair.testIndex(), false);
+ pairSearch.skipRemainingPairsForTestPosition();
}
+ remover.removeMarkedElements(x_solvent);
+ if (!v_solvent->empty())
+ {
+ remover.removeMarkedElements(v_solvent);
+ }
+ remover.removeMarkedElements(r);
+ const int originalAtomCount = atoms->nr;
+ remover.removeMarkedAtoms(atoms);
+ fprintf(stderr, "Removed %d solvent atoms more than %f nm from solute.\n",
+ originalAtomCount - atoms->nr, rshell);
+}
+
+/*! \brief
+ * Removes solvent molecules that overlap with the solute.
+ *
+ * \param[in,out] atoms Solvent atoms.
+ * \param[in,out] x Solvent positions.
+ * \param[in,out] v Solvent velocities (can be empty).
+ * \param[in,out] r Solvent exclusion radii.
+ * \param[in] pbc PBC information.
+ * \param[in] x_solute Solute positions.
+ * \param[in] r_solute Solute exclusion radii.
+ */
+static void removeSolventOverlappingWithSolute(t_atoms *atoms,
+ std::vector<RVec> *x,
+ std::vector<RVec> *v,
+ std::vector<real> *r,
+ const t_pbc &pbc,
+ const std::vector<RVec> &x_solute,
+ const std::vector<real> &r_solute)
+{
+ gmx::AtomsRemover remover(*atoms);
+ const real maxRadius1
+ = *std::max_element(r->begin(), r->end());
+ const real maxRadius2
+ = *std::max_element(r_solute.begin(), r_solute.end());
+ // Now check for overlap.
gmx::AnalysisNeighborhood nb;
- nb.setCutoff(std::max(maxRadius1 + maxRadius2, rshell));
+ gmx::AnalysisNeighborhoodPair pair;
+ nb.setCutoff(maxRadius1 + maxRadius2);
gmx::AnalysisNeighborhoodPositions posSolute(x_solute);
gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, posSolute);
gmx::AnalysisNeighborhoodPositions pos(*x);
gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
- gmx::AnalysisNeighborhoodPair pair;
while (pairSearch.findNextPair(&pair))
{
if (remover.isMarked(pair.testIndex()))
}
if (top->atoms.nr > 0)
{
- removeSoluteOverlap(atoms_solvt, &x_solvt, &v_solvt, &exclusionDistances_solvt, pbc,
- *x, exclusionDistances, rshell);
+ if (rshell > 0.0)
+ {
+ removeSolventOutsideShell(atoms_solvt, &x_solvt, &v_solvt,
+ &exclusionDistances_solvt, pbc, *x, rshell);
+ }
+ removeSolventOverlappingWithSolute(atoms_solvt, &x_solvt, &v_solvt,
+ &exclusionDistances_solvt, pbc, *x,
+ exclusionDistances);
}
if (max_sol > 0 && atoms_solvt->nres > max_sol)
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-o">
+ <GroFile Name="Header">
+ <String Name="Title">Generated by gmx solvate</String>
+ <Int Name="Number of atoms">141</Int>
+ </GroFile>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-o">
+ <GroFile Name="Header">
+ <String Name="Title">Test system for solvate/insert-molecules</String>
+ <Int Name="Number of atoms">2664</Int>
+ </GroFile>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-o">
+ <GroFile Name="Header">
+ <String Name="Title">Test system for solvate/insert-molecules</String>
+ <Int Name="Number of atoms">2664</Int>
+ </GroFile>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-o">
+ <GroFile Name="Header">
+ <String Name="Title">Test system for solvate/insert-molecules</String>
+ <Int Name="Number of atoms">762</Int>
+ </GroFile>
+ </File>
+ </OutputFiles>
+</ReferenceData>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, 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/gmxpreprocess/solvate.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/textreader.h"
#include "testutils/cmdlinetest.h"
+#include "testutils/conftest.h"
+#include "testutils/refdata.h"
#include "testutils/testfilemanager.h"
#include "testutils/textblockmatchers.h"
{
using gmx::test::CommandLine;
-using gmx::test::NoTextMatch;
+using gmx::test::ConfMatch;
class SolvateTest : public gmx::test::CommandLineTestBase
{
public:
SolvateTest()
{
- setOutputFile("-o", "out.gro", NoTextMatch());
+ setOutputFile("-o", "out.gro", ConfMatch());
}
void runTest(const CommandLine &args)
cmdline.merge(args);
ASSERT_EQ(0, gmx_solvate(cmdline.argc(), cmdline.argv()));
+ checkOutputFiles();
}
};
runTest(CommandLine(cmdline));
}
+TEST_F(SolvateTest, shell_Works)
+{
+ // use default solvent box (-cs without argument)
+ const char *const cmdline[] = {
+ "solvate", "-cs"
+ };
+ setInputFile("-cp", "spc-and-methanol.gro");
+ commandLine().addOption("-shell", 1.0);
+
+ runTest(CommandLine(cmdline));
+}
+
} // namespace
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2011,2012,2013,2014,2015,2016,2017, 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_directories(BEFORE SYSTEM ${GMOCK_INCLUDE_DIRS})
set(TESTUTILS_SOURCES
cmdlinetest.cpp
+ conftest.cpp
integrationtests.cpp
interactivetest.cpp
mpi-printer.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, 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.
+ */
+/*! \internal \file
+ * \brief
+ * Implements routine to check the content of conf files.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_testutils
+ */
+#include "gmxpre.h"
+
+#include "conftest.h"
+
+#include <cstdio>
+#include <cstdlib>
+
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textstream.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/textblockmatchers.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+namespace
+{
+
+class ConfMatcher : public ITextBlockMatcher
+{
+ public:
+ explicit ConfMatcher(const ConfMatchSettings &settings) : settings_(settings)
+ {
+ }
+
+ virtual void checkStream(TextInputStream *stream,
+ TestReferenceChecker *checker)
+ {
+ checkConfFile(stream, checker, settings_);
+ }
+ private:
+ ConfMatchSettings settings_;
+};
+
+} // namespace
+
+void checkConfFile(TextInputStream *input,
+ TestReferenceChecker *checker,
+ const ConfMatchSettings &)
+{
+
+ TestReferenceChecker groChecker(checker->checkCompound("GroFile", "Header"));
+ // Just check the first two lines of the output file
+ std::string line;
+ EXPECT_TRUE(input->readLine(&line));
+ line = stripSuffixIfPresent(line, "\n");
+ groChecker.checkString(line, "Title");
+ EXPECT_TRUE(input->readLine(&line));
+ line = stripSuffixIfPresent(line, "\n");
+ groChecker.checkInteger(std::atoi(line.c_str()), "Number of atoms");
+}
+
+TextBlockMatcherPointer ConfMatch::createMatcher() const
+{
+ return TextBlockMatcherPointer(new ConfMatcher(settings_));
+}
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, 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.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares function to add the content of a conf file to a checker.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+#ifndef GMX_TESTUTILS_CONFTEST_H
+#define GMX_TESTUTILS_CONFTEST_H
+
+#include <string>
+
+#include "testutils/testasserts.h"
+#include "testutils/textblockmatchers.h"
+
+namespace gmx
+{
+
+class TextInputStream;
+
+namespace test
+{
+
+class TestReferenceChecker;
+
+struct ConfMatchSettings
+{
+ ConfMatchSettings() : tolerance(defaultRealTolerance())
+ {
+ }
+
+ FloatingPointTolerance tolerance;
+};
+
+/*! \brief
+ * Adds content of a gro file to TestReferenceChecker object.
+ *
+ * \param[in] input Stream that provides the gro content.
+ * \param[in,out] checker Checker to use.
+ * \param[in] settings Settings to use for matching.
+ *
+ * Parses a gro file from the input stream, and checks the contents against
+ * reference data (only first two lines for now).
+ *
+ * \see ConfMatch
+ */
+void checkConfFile(TextInputStream *input,
+ TestReferenceChecker *checker,
+ const ConfMatchSettings &settings);
+
+/*! \libinternal \brief
+ * Match the contents as an gro file.
+ *
+ * \see checkGroFile()
+ *
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class ConfMatch : public ITextBlockMatcherSettings
+{
+ public:
+ //! Sets the tolerance for matching floating point values.
+ ConfMatch &tolerance(const FloatingPointTolerance &tolerance)
+ {
+ settings_.tolerance = tolerance;
+ return *this;
+ }
+
+ virtual TextBlockMatcherPointer createMatcher() const;
+
+ private:
+ ConfMatchSettings settings_;
+};
+
+} // namespace test
+
+} // namespace gmx
+
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff