/* Build using clang analyzer */
#cmakedefine01 GMX_CLANG_ANALYZER
-/* Use MiMiC QM/MM interface */
-#cmakedefine01 GMX_MIMIC
-
/* Use Interactive Molecular Dynamics */
#cmakedefine01 GMX_IMD
if (MASTER(cr))
{
- MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
+ MimicCommunicator::getCoords(state_global->x, state_global->natoms);
}
if (ir->efep != FreeEnergyPerturbationType::No)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2018,2019,2020,2021, 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.
# Set up the module library
add_library(mimic INTERFACE)
-file(GLOB MIMIC_SOURCES *.cpp)
+if (GMX_MIMIC)
+ file(GLOB MIMIC_SOURCES
+ communicator.cpp
+ utilities.cpp
+ )
+else()
+ file(GLOB MIMIC_SOURCES
+ communicator_stub.cpp
+ utilities.cpp
+ )
+endif()
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${MIMIC_SOURCES} PARENT_SCOPE)
# Source files have the following dependencies on library infrastructure.
#include <unordered_set>
#include "gromacs/math/units.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/arrayref.h"
-#if GMX_MIMIC
-# include <DataTypes.h>
-# include <MessageApi.h>
-#endif
+// Include headers from MiMiC library
+#include <DataTypes.h>
+#include <MessageApi.h>
-// When not built in a configuration with QMMM support, much of this
-// code is unreachable by design. Tell clang not to warn about it.
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wmissing-noreturn"
-
-#if !GMX_MIMIC
-//! \brief Definitions to stub the ones defined in DataTypes.h
-constexpr int TYPE_INT = 0, TYPE_DOUBLE = 0;
-
-/*! \brief Stub communication library function to call in case if
- * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
- */
-static void MCL_init_client(const char*) // NOLINT(readability-named-parameter)
+namespace gmx
{
- GMX_RELEASE_ASSERT(
- GMX_MIMIC,
- "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
-}
-/*! \brief Stub communication library function to call in case if
- * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
- */
-static void MCL_send(void*, int, int, int) // NOLINT(readability-named-parameter)
-{
- GMX_RELEASE_ASSERT(
- GMX_MIMIC,
- "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
-}
-
-/*! \brief Stub communication library function to call in case if
- * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
- */
-static void MCL_receive(void*, int, int, int) // NOLINT(readability-named-parameter)
-{
- GMX_RELEASE_ASSERT(
- GMX_MIMIC,
- "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
-}
-
-/*! \brief Stub communication library function to call in case if
- * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
- */
-static void MCL_destroy()
-{
- GMX_RELEASE_ASSERT(
- GMX_MIMIC,
- "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
-}
-#endif
-
-void gmx::MimicCommunicator::init()
+void MimicCommunicator::init()
{
char path[GMX_PATH_MAX];
gmx_getcwd(path, GMX_PATH_MAX);
MCL_init_client(path);
}
-void gmx::MimicCommunicator::sendInitData(gmx_mtop_t* mtop, PaddedHostVector<gmx::RVec> coords)
+void MimicCommunicator::sendInitData(gmx_mtop_t* mtop, ArrayRef<const RVec> coords)
{
MCL_send(&mtop->natoms, 1, TYPE_INT, 0);
MCL_send(&mtop->atomtypes.nr, 1, TYPE_INT, 0);
bonds.push_back(offset + at1 + 1);
bonds.push_back(offset + at2 + 1);
bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA)
- / gmx::c_bohr2Nm);
+ / c_bohr2Nm);
}
for (int ncon = 0; ncon < nsettle; ++ncon)
MCL_send(&*convertedCoords.begin(), 3 * mtop->natoms, TYPE_DOUBLE, 0);
}
-int64_t gmx::MimicCommunicator::getStepNumber()
+int64_t MimicCommunicator::getStepNumber()
{
int steps;
MCL_receive(&steps, 1, TYPE_INT, 0);
return steps;
}
-void gmx::MimicCommunicator::getCoords(PaddedHostVector<RVec>* x, const int natoms)
+void MimicCommunicator::getCoords(ArrayRef<RVec> x, const int natoms)
{
std::vector<double> coords(natoms * 3);
MCL_receive(&*coords.begin(), 3 * natoms, TYPE_DOUBLE, 0);
for (int j = 0; j < natoms; ++j)
{
- (*x)[j][0] = static_cast<real>(coords[j * 3] * gmx::c_bohr2Nm);
- (*x)[j][1] = static_cast<real>(coords[j * 3 + 1] * gmx::c_bohr2Nm);
- (*x)[j][2] = static_cast<real>(coords[j * 3 + 2] * gmx::c_bohr2Nm);
+ x[j][0] = static_cast<real>(coords[j * 3] * gmx::c_bohr2Nm);
+ x[j][1] = static_cast<real>(coords[j * 3 + 1] * gmx::c_bohr2Nm);
+ x[j][2] = static_cast<real>(coords[j * 3 + 2] * gmx::c_bohr2Nm);
}
}
-void gmx::MimicCommunicator::sendEnergies(real energy)
+void MimicCommunicator::sendEnergies(real energy)
{
double convertedEnergy = energy / (gmx::c_hartree2Kj * gmx::c_avogadro);
MCL_send(&convertedEnergy, 1, TYPE_DOUBLE, 0);
}
-void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
+void MimicCommunicator::sendForces(ArrayRef<RVec> forces, int natoms)
{
std::vector<double> convertedForce;
for (int j = 0; j < natoms; ++j)
MCL_send(&*convertedForce.begin(), convertedForce.size(), TYPE_DOUBLE, 0);
}
-void gmx::MimicCommunicator::finalize()
+void MimicCommunicator::finalize()
{
MCL_destroy();
}
-#pragma GCC diagnostic pop
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, 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.
#ifndef GMX_MIMIC_COMMUNICATOR_H
#define GMX_MIMIC_COMMUNICATOR_H
-#include "gromacs/gpu_utils/hostallocator.h"
-#include "gromacs/math/paddedvector.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/futil.h"
namespace gmx
{
+
+template<class T>
+class ArrayRef;
+
/**
* \inlibraryapi
* \internal \brief
* @param mtop global topology data
* @param coords coordinates of all atoms
*/
- static void sendInitData(gmx_mtop_t* mtop, PaddedHostVector<gmx::RVec> coords);
+ static void sendInitData(gmx_mtop_t* mtop, ArrayRef<const RVec> coords);
/*! \brief
* Gets the number of MD steps to perform from MiMiC
* @param x array of coordinates to fill
* @param natoms number of atoms in the system
*/
- static void getCoords(PaddedHostVector<RVec>* x, int natoms);
+ static void getCoords(ArrayRef<RVec> x, int natoms);
/*! \brief
* Send the potential energy value to MiMiC
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018,2019,2020,2021, 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.
+ *
+ * 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 "communicator.h"
+
+#include "gromacs/math/units.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
+
+namespace gmx
+{
+
+#ifdef __clang__
+# pragma clang diagnostic push
+# pragma clang diagnostic ignored "-Wmissing-noreturn"
+#endif
+
+void MimicCommunicator::init()
+{
+ GMX_THROW(InternalError(
+ "GROMACS is compiled without MiMiC support! Please, reconfigure with -DGMX_MIMIC=ON"));
+}
+
+void MimicCommunicator::sendInitData(gmx_mtop_t* /*mtop*/, ArrayRef<const RVec> /*coords*/)
+{
+ GMX_THROW(InternalError(
+ "GROMACS is compiled without MiMiC support! Please, reconfigure with -DGMX_MIMIC=ON"));
+}
+
+int64_t MimicCommunicator::getStepNumber()
+{
+ GMX_THROW(InternalError(
+ "GROMACS is compiled without MiMiC support! Please, reconfigure with -DGMX_MIMIC=ON"));
+}
+
+void MimicCommunicator::getCoords(ArrayRef<RVec> /*x*/, const int /*natoms*/)
+{
+ GMX_THROW(InternalError(
+ "GROMACS is compiled without MiMiC support! Please, reconfigure with -DGMX_MIMIC=ON"));
+}
+
+void MimicCommunicator::sendEnergies(real /*energy*/)
+{
+ GMX_THROW(InternalError(
+ "GROMACS is compiled without MiMiC support! Please, reconfigure with -DGMX_MIMIC=ON"));
+}
+
+void MimicCommunicator::sendForces(ArrayRef<RVec> /*forces*/, int /*natoms*/)
+{
+ GMX_THROW(InternalError(
+ "GROMACS is compiled without MiMiC support! Please, reconfigure with -DGMX_MIMIC=ON"));
+}
+
+void MimicCommunicator::finalize()
+{
+ GMX_THROW(InternalError(
+ "GROMACS is compiled without MiMiC support! Please, reconfigure with -DGMX_MIMIC=ON"));
+}
+
+#ifdef __clang__
+# pragma clang diagnostic pop
+#endif
+
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff