+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2016, 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 classes in mdruncomparisonfixture.h.
- *
- * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_mdrun_integration_tests
- */
-#include "gmxpre.h"
-
-#include "mdruncomparisonfixture.h"
-
-#include <map>
-#include <string>
-#include <utility>
-#include <vector>
-
-#include "gromacs/utility/stringutil.h"
-
-#include "testutils/testasserts.h"
-
-namespace gmx
-{
-namespace test
-{
-
-MdrunComparisonFixture::~MdrunComparisonFixture()
-{
-}
-
-namespace
-{
-
-//! Helper typedef
-typedef std::map<std::string, MdrunComparisonFixture::MdpFieldValues> MdpFileValues;
-
-//! Database of .mdp strings that supports MdrunComparisonFixture::prepareSimulation()
-MdpFileValues mdpFileValueDatabase_g
-{
- // Simple system with 12 argon atoms, fairly widely separated
- {
- "argon12", { {
- "ref-t", "80"
- },
- {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- } }
- },
- // Simple system with 5 water molecules, fairly widely separated
- {
- "spc5", { {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- } }
- },
- // Simple system with 5832 argon atoms, suitable for normal pressure coupling
- {
- "argon5832", { {
- "ref-t", "80"
- } }
- },
- // Simple system with 216 water molecules, condensed phase
- {
- "spc216", { }
- },
- // Capped alanine peptide in vacuo with virtual sites
- {
- "alanine_vsite_vacuo", { {
- "constraints", "all-bonds"
- },
- {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- } }
- },
- // Capped alanine peptide in aqueous condensed phase, with virtual sites
- {
- "alanine_vsite_solvated", { {
- "constraints", "all-bonds"
- } }
- },
- // Nonanol molecule in vacuo, topology suitable for FEP testing
- {
- "nonanol_vacuo", { {
- "nsteps", "16"
- },
- {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- },
- {
- "constraints", "h-bonds"
- },
- {
- "other",
- "free-energy = yes\n"
- "sc-alpha = 0.5\n"
- "sc-r-power = 6\n"
- "nstdhdl = 4\n"
- "init-lambda-state = 3\n"
- "fep_lambdas = 0.00 0.50 1.00 1.00 1.00\n"
- "vdw_lambdas = 0.00 0.00 0.00 0.50 1.00\n"
- "couple-moltype = nonanol\n"
- "couple-lambda0 = vdw-q\n"
- "couple-lambda1 = none\n"
- "couple-intramol = yes\n"
- } }
- }
-};
-
-} // namespace
-
-MdrunComparisonFixture::MdpFieldValues MdrunComparisonFixture::prepareMdpFieldValues(const char *simulationName)
-{
- /* Insert suitable .mdp defaults, so that the database set up
- * above does not need to specify redundant values. This works
- * because std::map.insert() does not over-write elements that
- * already exist.
- *
- * TODO ideally some of these default values should be the same as
- * grompp uses, and sourced from the same place, but that code is
- * a bit of a jungle. */
-
- typedef MdpFieldValues::value_type MdpField;
-
- auto &mdpFieldValues = mdpFileValueDatabase_g.at(simulationName);
- mdpFieldValues.insert(MdpField("nsteps", "16"));
- mdpFieldValues.insert(MdpField("ref-t", "298"));
- mdpFieldValues.insert(MdpField("tau-p", "1"));
- mdpFieldValues.insert(MdpField("compressibility", "5e-5"));
- mdpFieldValues.insert(MdpField("constraints", "none"));
- mdpFieldValues.insert(MdpField("other", ""));
-
- return mdpFieldValues;
-}
-
-void MdrunComparisonFixture::prepareMdpFile(const MdpFieldValues &mdpFieldValues,
- const char *integrator,
- const char *tcoupl,
- const char *pcoupl)
-{
- /* Set up an .mdp file that permits a highly reproducible
- * simulation. The format string needs to be configured with
- * values for various .mdp fields to suit the kind of system
- * used and testing needed. It also
- * - writes frames from different kinds of steps: starting, ending, intermediate NS, intermediate non-NS
- * - has other steps between frame-writing steps
- * - has enough buffer that e.g. a rerun will compute the same potential energy even though it does NS every frame
- * - has very slow pressure coupling and weak compressibility (since otherwise the box will shrink too fast)
- * - can have arbitrary chunks of .mdp content appended to it (but it is up to grompp how it deals with duplicate fields)
- * - sets random seeds to known values
- * - uses cutoffs that fit inside boxes even after GPU mdrun scales rlist
- *
- * Note that forces computed in the absence of energy computations
- * generally follow a different code path from those computed with
- * energies. However a rerun always computes energies, so we don't
- * currently have a good way to compare forces at steps where
- * energies were not computed with those from rerun on the same
- * coordinates.
- */
- runner_.useStringAsMdpFile(formatString("rcoulomb = 0.7\n"
- "rvdw = 0.7\n"
- "rlist = -1\n"
- "bd-fric = 1000\n"
- "verlet-buffer-tolerance = 0.000001\n"
- "nsteps = %s\n"
- "nstenergy = 4\n"
- "nstlist = 8\n"
- "nstxout = 4\n"
- "nstvout = 4\n"
- "nstfout = 4\n"
- "integrator = %s\n"
- "ld-seed = 234262\n"
- "tcoupl = %s\n"
- "ref-t = %s\n"
- "tau-t = 1\n"
- "tc-grps = System\n"
- "pcoupl = %s\n"
- "pcoupltype = isotropic\n"
- "ref-p = 1\n"
- "tau-p = %s\n"
- "compressibility = %s\n"
- "constraints = %s\n"
- "constraint-algorithm = lincs\n"
- "lincs-order = 2\n"
- "lincs-iter = 5\n"
- "%s",
- mdpFieldValues.at("nsteps").c_str(),
- integrator, tcoupl,
- mdpFieldValues.at("ref-t").c_str(),
- pcoupl,
- mdpFieldValues.at("tau-p").c_str(),
- mdpFieldValues.at("compressibility").c_str(),
- mdpFieldValues.at("constraints").c_str(),
- mdpFieldValues.at("other").c_str()));
-}
-
-void MdrunComparisonFixture::runTest(const char *simulationName,
- const char *integrator,
- const char *tcoupl,
- const char *pcoupl,
- FloatingPointTolerance tolerance)
-{
- CommandLine caller;
- caller.append("grompp");
- runTest(caller, simulationName, integrator, tcoupl, pcoupl, tolerance);
-}
-
-} // namespace test
-} // namespace gmx
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2016, 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
- *
- * \brief Functionality for testing whether calls to mdrun produce the
- * same energy and force quantities when they should do so.
- */
-#ifndef GMX_MDRUN_TESTS_MDRUNCOMPARISONFIXTURE_H
-#define GMX_MDRUN_TESTS_MDRUNCOMPARISONFIXTURE_H
-
-#include <map>
-#include <string>
-#include <utility>
-#include <vector>
-
-#include <gtest/gtest.h>
-
-#include "testutils/cmdlinetest.h"
-
-#include "moduletest.h"
-
-namespace gmx
-{
-
-namespace test
-{
-
-class EnergyFrame;
-class TrajectoryFrame;
-class FloatingPointTolerance;
-
-/*! \libinternal
- * \brief Declares abstract base text fixture class for integration
- * tests of mdrun functionality that will compare multiple calls to
- * mdrun.
- *
- * An internal database of several kinds of simulation useful for such
- * comparisons is available.
- *
- * Any method in this class may throw std::bad_alloc if out of memory.
- *
- * \ingroup module_mdrun_integration_tests
- */
-class MdrunComparisonFixture : public MdrunTestFixture
-{
- public:
- //! Destructor
- virtual ~MdrunComparisonFixture();
- //! Helper typedef
- typedef std::map<std::string, std::string> MdpFieldValues;
- /*! \brief Prepare .mdp values to do a simulation
- *
- * A database of several kinds of simulation useful for different
- * kinds of tests is available.
- * - argon12
- * - argon5832
- * - spc5
- * - spc216
- * - alanine_vsite_vacuo
- * - alanine_vsite_solvated
- * - nonanol
- *
- * Some of these systems are pretty minimal, because having
- * few atoms means few interactions, highly reproducible
- * forces, and allows tests to focus on the correctness of the
- * implementation of high-level mdrun features. The boxes are
- * of a reasonable size so that domain decomposition is
- * possible. The pressure-coupling parameters are isotropic,
- * and set up so that there will not be dramatic collapse of
- * volume over the handful of MD steps that will be run. A
- * single temperature-coupling group is used.
- *
- * This is separate from prepareMdpFile, so that derived
- * classes can react to the .mdp settings, e.g. by stopping a
- * run after half the steps.
- *
- * \throws std::bad_alloc if out of memory
- * std::out_of_range if \c simulationName is not in the database */
- MdpFieldValues prepareMdpFieldValues(const char *simulationName);
- /*! \brief Set up an .mdp file that permits a highly reproducible
- * simulation.
- *
- * \throws std::bad_alloc if out of memory */
- void prepareMdpFile(const MdpFieldValues &mdpFieldValues,
- const char *integrator,
- const char *tcoupl,
- const char *pcoupl);
- /*! \brief Run mdrun two ways in a test. Subclasses must override this method.
- *
- * It is expected that this method calls
- * prepareMdpFieldValues() and prepareMdpFile() to help set up
- * a call to grompp with gromppCallerRef. Then mdrun will be
- * called and perhaps energies and forces compared. */
- virtual void runTest(const CommandLine &gromppCallerRef,
- const char *simulationName,
- const char *integrator,
- const char *tcoupl,
- const char *pcoupl,
- FloatingPointTolerance tolerance) = 0;
- //! Convenience overload of runTest() for cases that don't need to customize the command line for grompp
- virtual void runTest(const char *simulationName,
- const char *integrator,
- const char *tcoupl,
- const char *pcoupl,
- FloatingPointTolerance tolerance);
-};
-
-} // namespace test
-} // namespace gmx
-
-#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff