if (GMXAPI)
add_subdirectory(gmxapi)
endif()
+
+add_subdirectory(nblib)
+if(GMX_INSTALL_NBLIB_API)
+ install(FILES
+ DESTINATION include/nblib)
+endif()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2020, 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.
+#
+# \author Victor Holanda <victor.holanda@cscs.ch>
+# \author Joe Jordan <ejjordan@kth.se>
+# \author Prashanth Kanduri <kanduri@cscs.ch>
+# \author Sebastian Keller <keller@cscs.ch>
+#
+
+# The following are copied directly from src/CMakeLists.txt
+set(IGNORED_CLANG_ALL_WARNINGS
+ "-Wno-c++98-compat -Wno-c++98-compat-pedantic" #No intention of C++98 compability
+ "-Wno-source-uses-openmp" #Don't warn for no-omp build
+ "-Wno-c++17-extensions" #Allowed in attributes (compilers are required to ignore unknown attributes)
+ "-Wno-documentation-unknown-command" #Custom commands are used
+ "-Wno-covered-switch-default" #GCC gives maybe-uninitialized without default label and checks for illegal enum values.
+ "-Wno-switch-enum" # default statement for enum is OK
+
+ # We need to use macros like
+ # GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR. Those will look strange
+ # if they don't have a semicolon after them, and might confuse
+ # tools like IDEs also.
+ "-Wno-extra-semi-stmt"
+
+ #Following ones are undecided/TODO
+ "-Wno-disabled-macro-expansion"
+ "-Wno-cast-align"
+ "-Wno-reserved-id-macro"
+ "-Wno-global-constructors"
+ "-Wno-exit-time-destructors"
+ "-Wno-unused-macros"
+ "-Wno-weak-vtables"
+ "-Wno-conditional-uninitialized"
+ "-Wno-format-nonliteral"
+ "-Wno-shadow"
+ "-Wno-cast-qual"
+ "-Wno-documentation"
+ "-Wno-used-but-marked-unused"
+ "-Wno-padded"
+ "-Wno-float-equal"
+ "-Wno-old-style-cast"
+ "-Wno-conversion"
+ "-Wno-double-promotion")
+string(REPLACE " " ";" IGNORED_CLANG_ALL_WARNINGS "${IGNORED_CLANG_ALL_WARNINGS}")
+
+set(TESTUTILS_DIR ${PROJECT_SOURCE_DIR}/src/testutils)
+include(${PROJECT_SOURCE_DIR}/src/testutils/TestMacros.cmake)
+
+# this allows all nblib tests to be run with "make check-nblib"
+add_custom_target(check-nblib
+ COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib
+ COMMENT "Running nblib tests"
+ USES_TERMINAL VERBATIM)
+
+add_library(nblib SHARED "")
+
+target_sources(nblib
+ PRIVATE
+ box.cpp
+ )
+
+set_target_properties(nblib
+ PROPERTIES
+ LINKER_LANGUAGE CXX
+ OUTPUT_NAME "nblib"
+ )
+
+target_link_libraries(nblib PRIVATE libgromacs)
+target_include_directories(nblib PRIVATE ${PROJECT_SOURCE_DIR}/api)
+include_directories(BEFORE ${CMAKE_SOURCE_DIR}/api)
+
+install(TARGETS nblib
+ EXPORT nblib
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ INCLUDES DESTINATION include
+ )
+
+if(GMX_INSTALL_NBLIB_API)
+ install(FILES
+ basicdefinitions.h
+ box.h
+ exception.h
+ forcecalculator.h
+ integrator.h
+ interactions.h
+ molecules.h
+ kerneloptions.h
+ nblib.h
+ particletype.h
+ simulationstate.h
+ topology.h
+ topologyhelpers.h
+ DESTINATION include/nblib)
+endif()
+
+add_subdirectory(util)
+
+if(BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements some definitions that are identical to those of gromacs
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ */
+#ifndef NBLIB_BASICDEFINITIONS_H
+#define NBLIB_BASICDEFINITIONS_H
+
+#include <cmath>
+
+// from utility/real.h
+#if GMX_DOUBLE
+# ifndef HAVE_REAL
+typedef double real;
+# define HAVE_REAL
+# endif
+#else /* GMX_DOUBLE */
+# ifndef HAVE_REAL
+typedef float real;
+# define HAVE_REAL
+# endif
+#endif /* GMX_DOUBLE */
+
+namespace nblib
+{
+
+namespace detail
+{
+// from math/units.h
+constexpr const float KILO = 1e3; /* Thousand */
+constexpr const double NANO = 1e-9; /* A Number */
+constexpr const double E_CHARGE = 1.602176634e-19; /* Exact definition, Coulomb NIST 2018 CODATA */
+constexpr const double BOLTZMANN = 1.380649e-23; /* (J/K, Exact definition, NIST 2018 CODATA */
+constexpr const double AVOGADRO = 6.02214076e23; /* 1/mol, Exact definition, NIST 2018 CODATA */
+constexpr const double RGAS = (BOLTZMANN * AVOGADRO); /* (J/(mol K)) */
+constexpr const double EPSILON0_SI = 8.8541878128e-12; /* F/m, NIST 2018 CODATA */
+constexpr const double EPSILON0 = ((EPSILON0_SI * NANO * KILO) / (E_CHARGE * E_CHARGE * AVOGADRO));
+
+// from pbc/ishift.h
+constexpr const int D_BOX_Z = 1;
+constexpr const int D_BOX_Y = 1;
+constexpr const int D_BOX_X = 2;
+constexpr const int N_BOX_Z = (2 * D_BOX_Z + 1);
+constexpr const int N_BOX_Y = (2 * D_BOX_Y + 1);
+constexpr const int N_BOX_X = (2 * D_BOX_X + 1);
+constexpr const int N_IVEC = (N_BOX_Z * N_BOX_Y * N_BOX_X);
+} // namespace detail
+
+//! Needed for generating Bolzmann velocity distribution (kJ/(mol K))
+constexpr const real BOLTZ = (detail::RGAS / detail::KILO); /* */
+
+//! Charge multiplication factor for Coulomb interactions
+constexpr const real ONE_4PI_EPS0 = (1.0 / (4.0 * M_PI * detail::EPSILON0));
+
+//! Conversion factor from degrees to radians
+constexpr const real DEG2RAD = M_PI / 180.0;
+
+//! The number of shift vectors needed for pbc
+constexpr const int numShiftVectors = detail::N_IVEC;
+
+// from math/vectypes.h
+constexpr const int dimX = 0; /* Defines for indexing in vectors */
+constexpr const int dimY = 1;
+constexpr const int dimZ = 2;
+
+constexpr const int dimSize = 3;
+typedef real rvec[dimSize];
+typedef real matrix[dimSize][dimSize];
+} // namespace nblib
+
+
+#endif // NBLIB_BASICDEFINITIONS_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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 nblib simulation box
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#include <cmath>
+
+#include "nblib/box.h"
+#include "nblib/exception.h"
+
+namespace nblib
+{
+
+Box::Box(real l) : Box(l, l, l) {}
+
+Box::Box(real x, real y, real z) : legacyMatrix_{ 0 }
+{
+ if (std::isnan(x) || std::isinf(x) || std::isnan(y) || std::isinf(y) || std::isnan(z) || std::isinf(z))
+ {
+ throw InputException("Cannot have NaN or Inf box length.");
+ }
+
+ legacyMatrix_[dimX][dimX] = x;
+ legacyMatrix_[dimY][dimY] = y;
+ legacyMatrix_[dimZ][dimZ] = z;
+}
+
+} // namespace nblib
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib simulation box
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#ifndef NBLIB_BOX_H
+#define NBLIB_BOX_H
+
+#include "nblib/basicdefinitions.h"
+
+namespace nblib
+{
+
+/*! \brief Box specifies the size of periodic simulation systems
+ *
+ * \inpublicapi
+ * \ingroup nblib
+ *
+ * Currently only cubic and rectangular boxes are supported.
+ *
+ */
+class Box final
+{
+public:
+ using LegacyMatrix = matrix;
+
+ //! Construct a cubic box.
+ explicit Box(real l);
+
+ //! Construct a rectangular box.
+ Box(real x, real y, real z);
+
+ //! Return the full matrix that specifies the box. Used for gromacs setup code.
+ [[nodiscard]] LegacyMatrix const& legacyMatrix() const { return legacyMatrix_; }
+
+private:
+ LegacyMatrix legacyMatrix_;
+};
+
+} // namespace nblib
+#endif // NBLIB_BOX_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib exception class
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#ifndef NBLIB_EXCEPTION_H
+#define NBLIB_EXCEPTION_H
+
+#include <exception>
+#include <string>
+
+namespace nblib
+{
+
+/*! \brief Base nblib exception class
+ *
+ * All nblib exceptions derive from this class and simply forward their message. This allows
+ * exceptions to be handled uniformly across different exception types.
+ */
+class NbLibException : public std::exception
+{
+public:
+ [[maybe_unused]] explicit NbLibException(const std::string& message) :
+ message_("NbLib Exception: " + message)
+ {
+ }
+
+ //! Overrides the what() in std::exception
+ [[nodiscard]] const char* what() const noexcept override { return message_.c_str(); }
+
+ //! Convenience call in case a string is wanted instead of a const char*
+ [[nodiscard]] const std::string& reason() const& { return message_; }
+
+private:
+ std::string message_;
+};
+
+/*! \brief The exception type for user input errors
+ *
+ * The message should give users some hint as to how to remedy the error.
+ */
+class InputException final : NbLibException
+{
+public:
+ using NbLibException::NbLibException;
+};
+
+} // namespace nblib
+#endif // NBLIB_EXCEPTION_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib ForceCalculator
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#ifndef NBLIB_FORCECALCULATOR_H
+#define NBLIB_FORCECALCULATOR_H
+
+#include "nblib/interactions.h"
+#include "nblib/kerneloptions.h"
+#include "nblib/simulationstate.h"
+
+namespace gmx
+{
+template<typename T>
+class ArrayRef;
+} // namespace gmx
+
+namespace nblib
+{
+class NbvSetupUtil;
+class GmxForceCalculator;
+
+/*! \brief Setups up and computes forces using gromacs backend.
+ *
+ * The ForceCalculator uses the data in the SimulationState and NBKernelOptions to opaquely
+ * construct all gromacs data structures needed to perform nonbonded force calculations. It is
+ * costly to create this object since much of the SimulationState and NBKernelOptions has to be
+ * passed to the gromacs backend. However, once constructed, compute can be called repeatedly only
+ * paying the cost of the actual nonbonded force calculation. Repeated calls to compute on the same
+ * coordinated will always return the same forces (within precision), so the user must update the
+ * positions using the forces generated here to advance a simulation. If the coordinates move
+ * sufficiently far from their positions at construction time, the efficiency of the calculation
+ * will suffer. To alleviate this, the user can call updatePairList.
+ *
+ */
+class ForceCalculator final
+{
+public:
+ ForceCalculator(const SimulationState& system, const NBKernelOptions& options);
+
+ ~ForceCalculator();
+
+ /*! \brief Dispatch the nonbonded force kernels and reduce the forces
+ *
+ * This function zeroes out all values in the passed in forces buffer, so it can be regarded as
+ * an output only param.
+ *
+ * \param[in] coordinates to be used for the force calculation
+ * \param[out] forces buffer to store the output forces
+ */
+ void compute(gmx::ArrayRef<const Vec3> coordinates, gmx::ArrayRef<Vec3> forces);
+
+ /*! \brief Puts particles on a grid based on bounds specified by the box
+ *
+ * As compute is called repeatedly, the particles drift apart and the force computation becomes
+ * progressively less efficient. Calling this function recomputes the particle-particle pair
+ * lists so that computation can proceed efficiently. Should be called around every 100 steps.
+ *
+ * \param particleInfoAllVdW The types of the particles to be placed on grids
+ * \param coordinates The coordinates to be placed on grids
+ * \param[in] box The system simulation box
+ */
+ void updatePairList(gmx::ArrayRef<const int> particleInfoAllVdW,
+ gmx::ArrayRef<Vec3> coordinates,
+ const Box& box);
+
+private:
+ //! GROMACS force calculator to compute forces
+ std::unique_ptr<GmxForceCalculator> gmxForceCalculator_;
+};
+
+} // namespace nblib
+
+#endif // NBLIB_FORCECALCULATOR_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib integrator
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ */
+#ifndef NBLIB_INTEGRATOR_H
+#define NBLIB_INTEGRATOR_H
+
+#include <vector>
+
+#include "nblib/box.h"
+#include "nblib/vector.h"
+
+namespace gmx
+{
+template<typename T>
+class ArrayRef;
+} // namespace gmx
+
+namespace nblib
+{
+
+class Topology;
+
+/*! \brief Simple integrator
+ *
+ */
+class LeapFrog final
+{
+public:
+ /*! \brief Constructor.
+ *
+ * \param[in] topology Topology object to build list of inverse masses.
+ * \param[in] box Box object for ensuring that coordinates remain within bounds
+ */
+ LeapFrog(const Topology& topology, const Box& box);
+
+ /*! \brief Integrate
+ *
+ * Integrates the equation of motion using Leap-Frog algorithm.
+ * Updates coordinates and velocities.
+ *
+ * \param[in] dt Timestep.
+ * \param[out] coordinates Coordinate array that would be modified in-place.
+ * \param[out] velocities Velocity array that would be modified in-place.
+ * \param[in] forces Force array to be read.
+ *
+ */
+ void integrate(real dt,
+ gmx::ArrayRef<Vec3> coordinates,
+ gmx::ArrayRef<Vec3> velocities,
+ gmx::ArrayRef<const Vec3> forces);
+
+private:
+ //! 1/mass for all atoms
+ std::vector<real> inverseMasses_;
+ //! Box for PBC conformity
+ Box box_;
+};
+
+} // namespace nblib
+
+#endif // NBLIB_INTEGRATOR_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib particle-types interactions
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ */
+#ifndef NBLIB_INTERACTIONS_H
+#define NBLIB_INTERACTIONS_H
+
+#include <map>
+#include <tuple>
+#include <unordered_map>
+
+#include "nblib/kerneloptions.h"
+#include "nblib/particletype.h"
+#include "nblib/util/user.h"
+
+namespace nblib
+{
+
+//! Shorthand for a map used for looking up non-bonded parameters using particle types
+//! Named type for the C6 parameter in the Lennard-Jones potential
+using C6 = StrongType<real, struct C6Parameter>;
+//! Named type for the C12 parameter in the Lennard-Jones potential
+using C12 = StrongType<real, struct C12Parameter>;
+
+using NonBondedInteractionMapImpl =
+ std::map<std::tuple<ParticleTypeName, ParticleTypeName>, std::tuple<C6, C12>>;
+
+//! Map used for looking up non-bonded parameters using particle types
+class NonBondedInteractionMap final
+{
+private:
+ using NamePairTuple = std::tuple<ParticleTypeName, ParticleTypeName>;
+ using ComboParameters = std::tuple<C6, C12>;
+ using InteractionMap = std::map<NamePairTuple, ComboParameters>;
+ InteractionMap interactionMap_;
+
+public:
+ void setInteractions(const ParticleTypeName&, const ParticleTypeName&, const C6, const C12);
+ size_t count(const NamePairTuple&);
+
+ [[nodiscard]] C6 getC6(const ParticleTypeName&, const ParticleTypeName&) const;
+ [[nodiscard]] C12 getC12(const ParticleTypeName&, const ParticleTypeName&) const;
+
+ InteractionMap::iterator begin() { return interactionMap_.begin(); }
+ InteractionMap::iterator end() { return interactionMap_.end(); }
+};
+
+/*! \brief Non-Bonded Interactions between Particle Types
+ *
+ * \inpublicapi
+ * \ingroup nblib
+ *
+ * A class to hold a mapping between pairs of particle types and the non-bonded
+ * interactions between them. One may add the non-bonded parameters, namely the
+ * C6/C12 params for each particle type individually and construct a pair-wise
+ * mapping using combination rules or manually specify the parameters between
+ * a specific pair.
+ *
+ */
+class ParticleTypesInteractions final
+{
+public:
+ //! Initialized with the default geometric combination rule
+ explicit ParticleTypesInteractions(CombinationRule = CombinationRule::Geometric);
+
+ //! Specify non-bonded params of a particle type
+ ParticleTypesInteractions& add(const ParticleTypeName& particleTypeName, C6 c6, C12 c12);
+
+ //! Specify the non-bonded params of a specific pair of particle types
+ ParticleTypesInteractions& add(const ParticleTypeName& particleTypeName1,
+ const ParticleTypeName& particleTypeName2,
+ C6 c6,
+ C12 c12);
+
+ //! Generate table based on the parameters stored
+ [[nodiscard]] NonBondedInteractionMap generateTable() const;
+
+ //! Get combination rule enabled in this object
+ [[nodiscard]] CombinationRule getCombinationRule() const;
+
+ //! Merge with the information stored in another ParticleTypesInteractions object
+ void merge(const ParticleTypesInteractions&);
+
+private:
+ CombinationRule combinationRule_;
+
+ std::map<ParticleTypeName, std::tuple<C6, C12>> singleParticleInteractionsMap_;
+ std::map<std::tuple<ParticleTypeName, ParticleTypeName>, std::tuple<C6, C12>> twoParticlesInteractionsMap_;
+};
+
+} // namespace nblib
+#endif // NBLIB_INTERACTIONS_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib kernel setup options
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#ifndef NBLIB_KERNELOPTIONS_H
+#define NBLIB_KERNELOPTIONS_H
+
+#include <memory>
+
+#include "nblib/basicdefinitions.h"
+
+namespace nblib
+{
+
+//! Enum for selecting the SIMD kernel type
+enum class SimdKernels : int
+{
+ SimdAuto,
+ SimdNo,
+ Simd4XM,
+ Simd2XMM,
+ Count
+};
+
+//! Enum for selecting the combination rule
+enum class CombinationRule : int
+{
+ Geometric,
+ LorentzBerthelot,
+ None,
+ Count
+};
+
+//! Enum for selecting coulomb type
+enum class CoulombType : int
+{
+ Pme,
+ Cutoff,
+ ReactionField,
+ Count
+};
+
+/*! \internal \brief
+ * The options for the nonbonded kernel caller
+ */
+struct NBKernelOptions final
+{
+ //! Whether to use a GPU, currently GPUs are not supported
+ bool useGpu = false;
+ //! The number of OpenMP threads to use
+ int numOpenMPThreads = 1;
+ //! The SIMD type for the kernel
+ SimdKernels nbnxmSimd = SimdKernels::SimdAuto;
+ //! The LJ combination rule
+ CombinationRule ljCombinationRule = CombinationRule::Geometric;
+ //! Use i-cluster half-LJ optimization for clusters with <= half LJ
+ bool useHalfLJOptimization = false;
+ //! The pairlist and interaction cut-off
+ real pairlistCutoff = 1.0;
+ //! Whether to compute energies (shift forces for virial are always computed on CPU)
+ bool computeVirialAndEnergy = false;
+ //! The Coulomb interaction function
+ CoulombType coulombType = CoulombType::Pme;
+ //! Whether to use tabulated PME grid correction instead of analytical, not applicable with simd=no
+ bool useTabulatedEwaldCorr = false;
+ //! The number of iterations for each kernel
+ int numIterations = 100;
+ //! Print cycles/pair instead of pairs/cycle
+ bool cyclesPerPair = false;
+ //! The time step
+ real timestep = 0.001;
+};
+
+} // namespace nblib
+
+#endif // NBLIB_KERNELOPTIONS_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \file
+ * \brief
+ * Implements nblib Molecule
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ *
+ * \inpublicapi
+ * \ingroup nblib
+ */
+#ifndef NBLIB_MOLECULES_H
+#define NBLIB_MOLECULES_H
+
+#include <string>
+#include <tuple>
+#include <unordered_map>
+#include <vector>
+
+#include "nblib/particletype.h"
+
+namespace nblib
+{
+//! Named type for unique identifier for a particle in a molecule
+using ParticleName = StrongType<std::string, struct ParticleNameParameter>;
+
+//! Named type for charges on a particle within a molecule
+using Charge = StrongType<real, struct ChargeParameter>;
+
+//! Named type for residue name used to diffentiate between sections of a molecule
+using ResidueName = StrongType<std::string, struct ResidueNameParameter>;
+
+//! Named type for the name of a molecule
+using MoleculeName = StrongType<std::string, struct MoleculeNameParameter>;
+
+struct ParticleData
+{
+ std::string particleName_;
+ std::string residueName_;
+ std::string particleTypeName_;
+ real charge_;
+};
+
+class Molecule final
+{
+public:
+ explicit Molecule(MoleculeName moleculeName);
+
+ //! Add a particle to the molecule with full specification of parameters.
+ Molecule& addParticle(const ParticleName& particleName,
+ const ResidueName& residueName,
+ const Charge& charge,
+ ParticleType const& particleType);
+
+ //! Add a particle to the molecule with implicit charge of 0
+ Molecule& addParticle(const ParticleName& particleName,
+ const ResidueName& residueName,
+ ParticleType const& particleType);
+
+ //! Add a particle to the molecule with residueName set using particleName
+ Molecule& addParticle(const ParticleName& particleName, const Charge& charge, ParticleType const& particleType);
+
+ //! Add a particle to the molecule with residueName set using particleName with implicit charge of 0
+ Molecule& addParticle(const ParticleName& particleName, ParticleType const& particleType);
+
+ // TODO: add exclusions based on the unique ID given to the particle of the molecule
+ void addExclusion(int particleIndex, int particleIndexToExclude);
+
+ //! Specify an exclusion with particle and residue names that have been added to molecule
+ void addExclusion(std::tuple<std::string, std::string> particle,
+ std::tuple<std::string, std::string> particleToExclude);
+
+ //! Specify an exclusion with particle names that have been added to molecule
+ void addExclusion(const std::string& particleName, const std::string& particleNameToExclude);
+
+ //! The number of molecules
+ int numParticlesInMolecule() const;
+
+ //! Return the ParticleType data for a specific particle name that has been added to the molecule
+ const ParticleType& at(const std::string& particlesTypeName) const;
+
+ //! Convert exclusions given by name to indices and unify with exclusions given by indices
+ //! returns a sorted vector containing no duplicates of particles to exclude by indices
+ std::vector<std::tuple<int, int>> getExclusions() const;
+
+ //! Return name of ith particle
+ ParticleName particleName(int i) const;
+
+ //! Return name of ith residue
+ ResidueName residueName(int i) const;
+
+ //! Return array of data structs on particle types
+ std::vector<ParticleData> particleData() const;
+
+ //! Return map of particle types and their names
+ std::unordered_map<std::string, ParticleType> particleTypesMap() const;
+
+ //! The molecule name
+ MoleculeName name() const;
+
+private:
+ //! Name of the molecule
+ MoleculeName name_;
+
+ //! one entry per particle in molecule
+ std::vector<ParticleData> particles_;
+
+ //! collection of distinct particle types in molecule
+ std::unordered_map<std::string, ParticleType> particleTypes_;
+
+ //! Used for calculated exclusions based on particle indices in molecule
+ std::vector<std::tuple<int, int>> exclusions_;
+
+ //! we cannot efficiently compute indices during the build-phase
+ //! so we delay the conversion until TopologyBuilder requests it
+ std::vector<std::tuple<std::string, std::string, std::string, std::string>> exclusionsByName_;
+};
+
+} // namespace nblib
+#endif // NBLIB_MOLECULES_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Aggregates nblib public API headers
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ */
+#ifndef NBLIB_HEADERS_H
+#define NBLIB_HEADERS_H
+
+#include "nblib/basicdefinitions.h"
+#include "nblib/box.h"
+#include "nblib/forcecalculator.h"
+#include "nblib/integrator.h"
+#include "nblib/interactions.h"
+#include "nblib/kerneloptions.h"
+#include "nblib/molecules.h"
+#include "nblib/particletype.h"
+#include "nblib/simulationstate.h"
+#include "nblib/topology.h"
+#include "nblib/topologyhelpers.h"
+#include "nblib/util/user.h"
+
+#endif // NBLIB_HEADERS_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \file
+ * \brief
+ * Declares nblib ParticleTypes
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ *
+ * \inpublicapi
+ * \ingroup nblib
+ */
+#ifndef NBLIB_PARTICLETYPE_H
+#define NBLIB_PARTICLETYPE_H
+
+#include <string>
+
+#include "nblib/util/user.h"
+
+namespace nblib
+{
+class TopologyBuilder;
+
+//! Named type for particle type name
+using ParticleTypeName = StrongType<std::string, struct ParticleTypeNameParameter>;
+//! Named type for particle mass
+using Mass = StrongType<real, struct MassParameter>;
+
+/*! \brief Class that represents the particle type.
+ *
+ * The particle type is used in lookup tables for masses, non-bonded parameters, etc.
+ * Every particle has to assigned an atom type.
+ */
+class ParticleType final
+{
+public:
+ /*! \brief Constructor with explicit name and mass specification.
+ *
+ * \param[in] name The unique name to reference the particle type.
+ * \param[in] mass The mass of the particle of this type.
+ */
+ ParticleType(ParticleTypeName name, Mass mass);
+
+ //! Get the type name
+ [[nodiscard]] ParticleTypeName name() const;
+
+ //! Get the mass
+ [[nodiscard]] Mass mass() const;
+
+private:
+ //! The name
+ ParticleTypeName name_;
+ //! The mass
+ Mass mass_;
+};
+
+/*! \brief Comparison operator
+ *
+ * \param[in] a First type.
+ * \param[in] b Second type.
+ * \returns If the types are identical.
+ */
+bool operator==(const ParticleType& a, const ParticleType& b);
+
+} // namespace nblib
+#endif // NBLIB_PARTICLETYPE_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib SimulationState
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ */
+#ifndef NBLIB_SIMULATIONSTATE_H
+#define NBLIB_SIMULATIONSTATE_H
+
+#include <memory>
+#include <vector>
+
+#include "nblib/box.h"
+#include "nblib/topology.h"
+
+namespace nblib
+{
+
+/*! \libinternal
+ * \ingroup nblib
+ * \brief Simulation State
+ *
+ * Simulation state description that serves as a snapshot of the system
+ * being analysed. Needed to init an MD program. Allows hot-starting simulations.
+ */
+
+class SimulationState final
+{
+public:
+ //! Constructor
+ SimulationState(const std::vector<Vec3>& coordinates,
+ const std::vector<Vec3>& velocities,
+ const std::vector<Vec3>& forces,
+ Box box,
+ Topology topology);
+
+ //! Returns topology of the current state
+ const Topology& topology() const;
+
+ //! Returns the box
+ Box box() const;
+
+ //! Returns a reference to a (modifiable) vector of particle coordinates
+ std::vector<Vec3>& coordinates();
+
+ //! Returns a read-only vector of particle coordinates
+ const std::vector<Vec3>& coordinates() const;
+
+ //! Returns a reference to a (modifiable) vector of particle velocities
+ std::vector<Vec3>& velocities();
+
+ //! Returns a reference to a (modifiable) vector of forces
+ std::vector<Vec3>& forces();
+
+private:
+ class Impl;
+ std::shared_ptr<SimulationState::Impl> simulationStatePtr_;
+};
+
+} // namespace nblib
+
+#endif // NBLIB_SIMULATIONSTATE_H
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2020, 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.
+#
+# \author Victor Holanda <victor.holanda@cscs.ch>
+# \author Joe Jordan <ejjordan@kth.se>
+# \author Prashanth Kanduri <kanduri@cscs.ch>
+# \author Sebastian Keller <keller@cscs.ch>
+#
+
+# Make a static library for test infrastructure code that we re-use
+# in multiple test executables across the repository.
+gmx_add_unit_test_library(nblib_test_infrastructure
+ testhelpers.cpp
+ )
+target_include_directories(nblib_test_infrastructure PRIVATE ${PROJECT_SOURCE_DIR}/api)
+target_include_directories(nblib_test_infrastructure SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+
+
+set(testname "NbLibSetupTests")
+set(exename "nblib-setup-test")
+
+gmx_add_gtest_executable(
+ ${exename}
+ CPP_SOURCE_FILES
+ # files with code for tests
+ box.cpp
+ )
+target_link_libraries(${exename} PRIVATE nblib_test_infrastructure nblib)
+target_include_directories(${exename} PRIVATE ${PROJECT_SOURCE_DIR}/api)
+gmx_register_gtest_test(${testname} ${exename} INTEGRATION_TEST)
+add_dependencies(check-nblib ${exename})
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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
+ * This implements basic nblib box tests
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#include <cmath>
+
+#include "nblib/box.h"
+#include "nblib/exception.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+using gmx::test::defaultRealTolerance;
+
+namespace nblib
+{
+
+TEST(NBlibTest, CubicBoxCannotHaveNaN)
+{
+ real number = NAN;
+ EXPECT_THROW(Box box(number), InputException);
+}
+
+TEST(NBlibTest, CubicBoxCannotHaveInf)
+{
+ real number = INFINITY;
+ EXPECT_THROW(Box box(number), InputException);
+}
+
+TEST(NBlibTest, RectangularBoxCannotHaveNaN)
+{
+ real number = NAN;
+ EXPECT_THROW(Box box(number, real(1.), real(1.)), InputException);
+}
+
+TEST(NBlibTest, RectangularBoxCannotHaveInf)
+{
+ real number = INFINITY;
+ EXPECT_THROW(Box box(number, real(1.), real(1.)), InputException);
+}
+
+TEST(NBlibTest, CubicBoxWorks)
+{
+ real length = 3;
+ Box::LegacyMatrix ref = { { length, 0, 0 }, { 0, length, 0 }, { 0, 0, length } };
+ Box test = Box(length);
+
+ for (int i = 0; i < dimSize; ++i)
+ for (int j = 0; j < dimSize; ++j)
+ EXPECT_REAL_EQ_TOL(ref[i][j], test.legacyMatrix()[i][j], defaultRealTolerance());
+}
+
+} // namespace nblib
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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
+ * This implements basic nblib test systems
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#include "nblib/tests/testhelpers.h"
+
+namespace nblib
+{
+namespace test
+{
+
+//! Compare between two instances of the Box object
+bool operator==(const Box& a, const Box& b)
+{
+ if (a.legacyMatrix()[XX][XX] != b.legacyMatrix()[XX][XX])
+ {
+ return false;
+ }
+ if (a.legacyMatrix()[YY][YY] != b.legacyMatrix()[YY][YY])
+ {
+ return false;
+ }
+ if (a.legacyMatrix()[ZZ][ZZ] != b.legacyMatrix()[ZZ][ZZ])
+ {
+ return false;
+ }
+ return true;
+}
+
+} // namespace test
+} // namespace nblib
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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
+ * This implements basic nblib test systems
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#ifndef NBLIB_TESTS_TESTHELPERS_H
+#define NBLIB_TESTS_TESTHELPERS_H
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
+#include "nblib/box.h"
+#include "nblib/vector.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace nblib
+{
+
+namespace test
+{
+
+//! Compare between two instances of the Box object
+bool operator==(const Box& a, const Box& b);
+
+/*! \internal \brief
+ * Simple test harness for checking 3D vectors like coordinates, velocities,
+ * forces against reference data
+ *
+ */
+class Vector3DTest
+{
+public:
+ Vector3DTest() : checker_(refData_.rootChecker())
+ {
+ gmx::test::FloatingPointTolerance tolerance(
+ gmx::test::FloatingPointTolerance(1e-8, 1.0e-12, 1e-8, 1.0e-12, 200, 100, true));
+ checker_.setDefaultTolerance(tolerance);
+ }
+
+ //! Compare a given input vector of cartesians with the reference data
+ void testVectors(gmx::ArrayRef<Vec3> forces, const std::string& testString)
+ {
+ checker_.checkSequence(forces.begin(), forces.end(), testString.c_str());
+ }
+
+private:
+ gmx::test::TestReferenceData refData_;
+ gmx::test::TestReferenceChecker checker_;
+};
+
+//! Macros to compare floats and doubles with a specified tolerance
+/// \cond DO_NOT_DOCUMENT
+#if GMX_DOUBLE
+# define EXPECT_FLOAT_DOUBLE_EQ_TOL(value, refFloat, refDouble, tolerance) \
+ EXPECT_DOUBLE_EQ_TOL(value, refDouble, tolerance)
+# define ASSERT_FLOAT_DOUBLE_EQ_TOL(value, refFloat, refDouble, tolerance) \
+ ASSERT_DOUBLE_EQ_TOL(value, refDouble, tolerance)
+#else
+# define EXPECT_FLOAT_DOUBLE_EQ_TOL(value, refFloat, refDouble, tolerance) \
+ EXPECT_FLOAT_EQ_TOL(value, refFloat, tolerance)
+# define ASSERT_FLOAT_DOUBLE_EQ_TOL(value, refFloat, refDouble, tolerance) \
+ ASSERT_FLOAT_EQ_TOL(value, refFloat, tolerance)
+#endif
+/// \endcond
+
+} // namespace test
+} // namespace nblib
+#endif // NBLIB_TESTS_TESTHELPERS_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib Topology and TopologyBuilder
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ */
+#ifndef NBLIB_TOPOLOGY_H
+#define NBLIB_TOPOLOGY_H
+
+#include <vector>
+
+#include "nblib/interactions.h"
+#include "nblib/molecules.h"
+#include "nblib/topologyhelpers.h"
+
+namespace gmx
+{
+template<typename>
+class ListOfLists;
+} // namespace gmx
+
+namespace nblib
+{
+
+/*! \inpublicapi
+ * \ingroup nblib
+ * \brief System Topology
+ *
+ * Contains all topology information meant to be used by the simulation
+ * engine internally. Private constructor ensures that a Topology object
+ * exists in a scope in a valid state after it has been built using a
+ * Topology Builder.
+ */
+class Topology final
+{
+
+public:
+ //! Returns the total number of particles in the system
+ int numParticles() const;
+
+ //! Returns a vector of particle types
+ std::vector<ParticleType> getParticleTypes() const;
+
+ //! Return the ParticleType ID of all particles
+ std::vector<int> getParticleTypeIdOfAllParticles() const;
+
+ //! Returns a vector of particles partial charges
+ std::vector<real> getCharges() const;
+
+ //! Returns exclusions in proper, performant, GROMACS layout
+ gmx::ListOfLists<int> getGmxExclusions() const;
+
+ //! Returns the unique ID of a specific particle belonging to a molecule in the global space
+ int sequenceID(MoleculeName moleculeName, int moleculeNr, ResidueName residueName, ParticleName particleName) const;
+
+ //! Returns a map of non-bonded force parameters indexed by ParticleType names
+ NonBondedInteractionMap getNonBondedInteractionMap() const;
+
+ //! Returns the combination rule used to generate the NonBondedInteractionMap
+ CombinationRule getCombinationRule() const;
+
+private:
+ Topology() = default;
+
+ friend class TopologyBuilder;
+
+ //! Total number of particles in the system
+ int numParticles_;
+ //! unique collection of ParticleTypes
+ std::vector<ParticleType> particleTypes_;
+ //! store an ID of each particles's type
+ std::vector<int> particleTypeIdOfAllParticles_;
+ //! Storage for particles partial charges
+ std::vector<real> charges_;
+ //! Information about exclusions.
+ gmx::ListOfLists<int> exclusions_;
+ //! Associate molecule, residue and particle names with sequence numbers
+ detail::ParticleSequencer particleSequencer_;
+ //! Map that should hold all nonbonded interactions for all particle types
+ NonBondedInteractionMap nonBondedInteractionMap_;
+ //! Combination Rule used to generate the nonbonded interactions
+ CombinationRule combinationRule_;
+};
+
+/*! \brief Topology Builder
+ *
+ * \libinternal
+ * \ingroup nblib
+ *
+ * A helper class to assist building of topologies. They also ensure that
+ * topologies only exist in a valid state within the scope of the
+ * simulation program.
+ *
+ */
+class TopologyBuilder final
+{
+public:
+ //! Constructor
+ TopologyBuilder();
+
+ /*! \brief
+ * Builds and Returns a valid Topology
+ *
+ * This function accounts for all the molecules added along with their
+ * exclusions and returns a topology with a valid state that is usable
+ * by the GROMACS back-end.
+ */
+ Topology buildTopology();
+
+ //! Adds a molecules of a certain type into the topology
+ TopologyBuilder& addMolecule(const Molecule& moleculeType, int nMolecules);
+
+ //! Add non-bonded interaction map to the topology
+ void addParticleTypesInteractions(const ParticleTypesInteractions& particleTypesInteractions);
+
+private:
+ //! Internally stored topology
+ Topology topology_;
+
+ //! Total number of particles in the system
+ int numParticles_;
+
+ //! List of molecule types and number of molecules
+ std::vector<std::tuple<Molecule, int>> molecules_;
+
+ //! Builds a GROMACS-compliant performant exclusions list aggregating exclusions from all molecules
+ gmx::ListOfLists<int> createExclusionsListOfLists() const;
+
+ //! Helper function to extract quantities like mass, charge, etc from the system
+ template<typename T, class Extractor>
+ std::vector<T> extractParticleTypeQuantity(Extractor&& extractor);
+
+ //! Distinct collection of ParticleTypes
+ std::unordered_map<std::string, ParticleType> particleTypes_;
+
+ //! ParticleType nonbonded parameters
+ ParticleTypesInteractions particleTypesInteractions_;
+};
+
+} // namespace nblib
+
+#endif // NBLIB_TOPOLOGY_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements helper functions needed for the nblib topology
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ */
+#ifndef NBLIB_TOPOLOGY_HELPERS_H
+#define NBLIB_TOPOLOGY_HELPERS_H
+
+#include <tuple>
+#include <unordered_map>
+#include <vector>
+
+#include "gromacs/utility/listoflists.h"
+#include "nblib/molecules.h"
+
+namespace gmx
+{
+struct ExclusionBlock;
+}
+
+namespace nblib
+{
+
+namespace detail
+{
+
+//! Converts tuples of particle indices to exclude to the gmx::ExclusionBlock format
+std::vector<gmx::ExclusionBlock> toGmxExclusionBlock(const std::vector<std::tuple<int, int>>& tupleList);
+
+//! Add offset to all indices in inBlock
+std::vector<gmx::ExclusionBlock> offsetGmxBlock(std::vector<gmx::ExclusionBlock> inBlock, int offset);
+
+//! Helper class for Topology to keep track of particle IDs
+class ParticleSequencer
+{
+ //! Alias for storing by (molecule name, molecule nr, residue name, particle name)
+ using DataType = std::unordered_map<
+ std::string,
+ std::unordered_map<int, std::unordered_map<std::string, std::unordered_map<std::string, int>>>>;
+
+public:
+ //! Build sequence from a list of molecules
+ void build(const std::vector<std::tuple<Molecule, int>>& moleculesList);
+
+ //! Access ID by (molecule name, molecule nr, residue name, particle name)
+ int operator()(const MoleculeName&, int, const ResidueName&, const ParticleName&) const;
+
+private:
+ DataType data_;
+};
+
+} // namespace detail
+
+} // namespace nblib
+
+#endif // NBLIB_TOPOLOGY_HELPERS_H
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2020, 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.
+#
+# \author Victor Holanda <victor.holanda@cscs.ch>
+# \author Joe Jordan <ejjordan@kth.se>
+# \author Prashanth Kanduri <kanduri@cscs.ch>
+# \author Sebastian Keller <keller@cscs.ch>
+#
+
+if(GMX_INSTALL_NBLIB_API)
+ install(FILES
+ user.h
+ DESTINATION include/nblib/util)
+endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib utilities
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ */
+
+#ifndef NBLIB_UTIL_USER_H
+#define NBLIB_UTIL_USER_H
+
+#include <functional>
+#include <iostream>
+#include <sstream>
+#include <string>
+#include <tuple>
+#include <type_traits>
+#include <vector>
+
+#include "nblib/basicdefinitions.h"
+#include "nblib/vector.h"
+
+namespace nblib
+{
+
+//! Generate velocities from a Maxwell Boltzmann distribution, masses should be the
+//! same as the ones specified for the Topology object
+std::vector<Vec3> generateVelocity(real Temperature, unsigned int seed, std::vector<real> const& masses);
+
+//! Check within the container of gmx::RVecs for a NaN or inf
+bool checkNumericValues(const std::vector<Vec3>& values);
+
+//! Used to ignore unused arguments of a lambda functions
+inline void ignore_unused() {}
+
+//! Variadic argument version of the ignore_unused function
+template<class T, class... Ts>
+inline void ignore_unused(T& x, Ts&... xs)
+{
+ static_cast<void>(x);
+ ignore_unused(xs...);
+}
+
+/*! \brief A template to create structs as a type-safe alternative to using declarations
+ *
+ * \inpublicapi
+ * \ingroup nblib
+ *
+ * Used in public API functions where a distinction between different
+ * arguments of the same underlying type is desired. This provides a type-safe
+ * version to using declarations. Instead of naming a type alias, the name
+ * is used to define a struct that inherits from StrongType<T>, where T is
+ * the underlying type. For example:
+ *
+ * struct C6 : StrongType<real>
+ * {
+ * using StrongType::StrongType;
+ * using StrongType::operator=;
+ * };
+ *
+ * Due to the T() conversion and assignment from T,
+ * an instance of the resulting C6 struct behaves essentially like a real, while construction
+ * from real is disabled. This makes it impossible to pass a real as a function parameter
+ * of type C6.
+ */
+template<class T, class Phantom>
+struct StrongType
+{
+ //! default ctor
+ StrongType() : value_{} {}
+ //! construction from the underlying type T, implicit conversions disabled
+ explicit StrongType(T v) : value_(std::move(v)) {}
+
+ //! assignment from T
+ StrongType& operator=(T v)
+ {
+ value_ = std::move(v);
+ return *this;
+ }
+
+ //! conversion to T
+ operator T() const { return value_; }
+
+ //! access the underlying value
+ T value() const { return value_; }
+
+private:
+ T value_;
+};
+
+//! Equality comparison. For the case where a comparison between StrongTypes with matching T, but differing Phantom
+//! parameters is desired, the underlying value attribute should be compared instead
+template<class T, class Phantom>
+[[maybe_unused]] inline bool operator==(const StrongType<T, Phantom>& lhs, const StrongType<T, Phantom>& rhs)
+{
+ return lhs.value() == rhs.value();
+}
+
+//! comparison function <
+template<class T, class Phantom>
+inline bool operator<(const StrongType<T, Phantom>& lhs, const StrongType<T, Phantom>& rhs)
+{
+ return lhs.value() < rhs.value();
+}
+
+//! comparison function >
+template<class T, class Phantom>
+inline bool operator>(const StrongType<T, Phantom>& lhs, const StrongType<T, Phantom>& rhs)
+{
+ return lhs.value() > rhs.value();
+}
+
+
+//! Base template for a holder of entries of different data types
+template<class... Ts>
+struct TypeList
+{
+};
+
+//! Base template for mapping between a datatype P templated separately with instances of type list L
+template<template<class...> class P, class L>
+struct Map_
+{
+};
+
+//! this is a specialization of the Map_ base template
+//! for the case that the L template parameter itself has template parameters
+//! in this case, the template parameters of L are caught in Ts...
+template<template<class...> class P, template<class...> class L, class... Ts>
+struct Map_<P, L<Ts...>>
+{
+ //! resulting type is a TypeList of the P-template instantiated
+ //! with all template parameters of L
+ typedef TypeList<P<Ts>...> type;
+};
+
+//! Maps a datatype P to create instances where each is templated with entries of type list L
+template<template<class...> class P, class L>
+using Map = typename Map_<P, L>::type;
+
+//! Base template for expressing a datatype P templated with all the entries in type list L
+template<template<class...> class P, class L>
+struct Reduce_
+{
+};
+
+//! Specialization of the Reduce_ base template
+template<template<class...> class P, template<class...> class L, class... Ts>
+struct Reduce_<P, L<Ts...>>
+{
+ //! resulting type is P instantiated
+ //! with all template parameters of L
+ typedef P<Ts...> type;
+};
+
+//! Expresses a data type P instantiated with all the entries in list L as template arguments
+template<template<class...> class P, class L>
+using Reduce = typename Reduce_<P, L>::type;
+
+} // namespace nblib
+
+#endif // NBLIB_UTIL_USER_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib Cartesian coordinate vector
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#ifndef NBLIB_BASICVECTOR_H
+#define NBLIB_BASICVECTOR_H
+
+#include "gromacs/math/vectypes.h"
+#include "nblib/basicdefinitions.h"
+
+namespace nblib
+{
+using Vec3 = gmx::BasicVector<real>;
+} // namespace nblib
+#endif // NBLIB_BASICVECTOR_H
)
endif ()
+ gmx_add_sphinx_source_files(
+ FILES
+ nblib/index.rst
+ nblib/guide-to-writing-MD-programs.rst
+ )
+
gmx_add_sphinx_source_files(
FILES
${REFERENCEMANUAL_SPHINX_FILES_GENERAL})
how-to/index
reference-manual/index
gmxapi/index
+ nblib/index
dev-manual/index
==================
how-to/index
reference-manual/index
gmxapi/index
+ nblib/index
dev-manual/index
--- /dev/null
+Guide to Writing MD Programs
+============================
+
+The goal of NB-LIB’s is to enable researchers to programmatically define molecular simulations.
+Traditionally these have been performed using a collection of executables and a manual workflow followed by a “black-box” simulation engine.
+NB-LIB allows users to script a variety of novel simulation and analysis workflows at a more granular level.
+
+Many possible use cases are facilitated by the flexibility that NB-LIB allows.
+These include customized update rules, defining custom forces, or orchestrating swarms of simulations.
+NB-LIB also allows for writing conventional MD simulations and analysis.
+
+This document goes over the steps to write MD programs using the API in NB-LIB that exposes features that are a part of the GROMACS package.
+
+Global Definitions
+------------------
+
+NB-LIB programs are written in C++ so its headers for I/O or advanced tasks must be included.
+In addition, one must include the headers for various capabilities and abstractions NB-LIB exposes as well.
+This can be directly copied from here.
+Finally, we use the namespace ``nblib`` for the data structures defined in the library.
+The last line in the block allows one to skip this specifier each time a function or a data structure is used.
+
+.. code:: cpp
+
+ #include <cstdio>
+
+ #include "nblib/box.h"
+ #include "nblib/forcecalculator.h"
+ #include "nblib/integrator.h"
+ #include "nblib/molecules.h"
+ #include "nblib/nbkerneloptions.h"
+ #include "nblib/particletype.h"
+ #include "nblib/simulationstate.h"
+ #include "nblib/topology.h"
+
+ using namespace nblib;
+
+Define Particle Data
+--------------------
+
+.. code:: cpp
+
+ // Parameters from a GROMOS compatible force-field 2016H66
+
+ struct OWaterAtom
+ {
+ ParticleName name = "Ow";
+ Mass mass = 15.999;
+ C6 c6 = 0.0026173456;
+ C12 c12 = 2.634129e-06;
+ };
+
+ struct HwAtom
+ {
+ ParticleName name = "Hw";
+ Mass mass = 1.00784;
+ C6 c6 = 0.0;
+ C12 c12 = 0.0;
+ };
+
+ struct CMethAtom
+ {
+ ParticleName name = "Cm";
+ Mass mass = 12.0107;
+ C6 c6 = 0.01317904;
+ C12 c12 = 34.363044e-06;
+ };
+
+ struct HcAtom
+ {
+ ParticleName name = "Hc";
+ Mass mass = 1.00784;
+ C6 c6 = 8.464e-05;
+ C12 c12 = 15.129e-09;
+ };
+
+There can be as many structs of this kind as there are particle types in the system.
+Organizing the data like this is not strictly necessary, but is shown for the purpose of clarity.
+As shown here, there can be multiple particles that correspond to a single element as atomic mass can vary by molecular context.
+For example, the carbon atom in a carboxyl group would have different parameters from one in the methyl group.
+We can obtain the parameter set from any standard force-field, or generate new parameters to study new compounds or force fields.
+This example comes from the `2016H66 Parameter Set <https://pubs.acs.org/doi/10.1021/acs.jctc.6b00187>`__.
+
+Defining Coordinates, Velocities and Force Buffers
+--------------------------------------------------
+
+.. code:: cpp
+
+ std::vector<gmx::RVec> coordinates = {
+ { 0.794, 1.439, 0.610 }, { 1.397, 0.673, 1.916 }, { 0.659, 1.080, 0.573 },
+ { 1.105, 0.090, 3.431 }, { 1.741, 1.291, 3.432 }, { 1.936, 1.441, 5.873 },
+ { 0.960, 2.246, 1.659 }, { 0.382, 3.023, 2.793 }, { 0.053, 4.857, 4.242 },
+ { 2.655, 5.057, 2.211 }, { 4.114, 0.737, 0.614 }, { 5.977, 5.104, 5.217 },
+ };
+
+ std::vector<gmx::RVec> velocities = {
+ { 0.0055, -0.1400, 0.2127 }, { 0.0930, -0.0160, -0.0086 }, { 0.1678, 0.2476, -0.0660 },
+ { 0.1591, -0.0934, -0.0835 }, { -0.0317, 0.0573, 0.1453 }, { 0.0597, 0.0013, -0.0462 },
+ { 0.0484, -0.0357, 0.0168 }, { 0.0530, 0.0295, -0.2694 }, { -0.0550, -0.0896, 0.0494 },
+ { -0.0799, -0.2534, -0.0079 }, { 0.0436, -0.1557, 0.1849 }, { -0.0214, 0.0446, 0.0758},
+ };
+
+ std::vector<gmx::RVec> forces = {
+ { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
+ { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
+ { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
+ { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
+ };
+
+We can initialize coordinates for our particles using ``std::vector`` of ``gmx::RVec`` which is a specific data type for holding 3D vector quantities. `Doxygen page on RVec here`__.
+
+ __ doxygen-ref-rvec_
+
+Writing the MD Program
+----------------------
+
+As with as any basic C++ program, there needs to be a ``main()`` function.
+
+
+Define ParticleTypes
+~~~~~~~~~~~~~~~~~~~~
+
+.. code:: cpp
+
+ int main()
+ {
+ // Bring the parameter structs to scope
+ OwAtom owAtom;
+ HwAtom hwAtom;
+ CMethAtom cmethAtom;
+ HcAtom hcAtom;
+
+ // Create the particles
+ ParticleType Ow(owAtom.name, owAtom.mass);
+ ParticleType Hw(hwAtom.name, hwAtom.mass);
+ ParticleType Cm(cmethAtom.name, cmethAtom.mass);
+ ParticleType Hc(hcAtom.name, hcAtom.mass);
+
+As before, the helper struct to define ``ParticleType`` data is not strictly needed, but is shown for clarity.
+The line ``ParticleType CMethAtom(ParticleName("Cm"), Mass(12.0107));`` would be sufficient.
+
+Define Non-Bonded Interactions
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code:: cpp
+
+ ParticleTypeInteractions interactions(CombinationRule::Geometric);
+
+ // add non-bonded interactions for the particle types
+ interactions.add(owAtom.name, owAtom.c6, owAtom.c12);
+ interactions.add(hwAtom.name, hwAtom.c6, hwAtom.c12);
+ interactions.add(cmethAtom.name, cmethAtom.c6, cmethAtom.c12);
+ interactions.add(hcAtom.name, hcAtom.c6, hcAtom.c12);
+
+For the Lennard-Jones interactions, we define a ``ParticleTypeInteractions`` object.
+Each particle of the ``ParticleType`` interacts with each other based on the ``C6`` and ``C12`` parameters.
+These parameters of the two different particles are averaged using ``Geometric`` or ``LorentzBerthelot`` ``CombinationRule``.
+More details `here <http://manual.gromacs.org/documentation/2019/reference-manual/functions/nonbonded-interactions.html#the-lennard-jones-interaction>`__.
+By default ``CombinationRule::Geometric`` is selected.
+
+We add the interaction parameters of each of the particle types into the ``ParticleTypeInteractions`` object.
+The result is a table that has interactions specified for all ``ParticleType`` pairs.
+The following matrix describes the pair-wise C6 parameter created using ``CombinationRule::Geometric``.
+
+== ====== === ======= =======
+# Ow Hw Cm Hc
+== ====== === ======= =======
+Ow 0.0026 0.0 0.42 4.7e-4
+Hw 0.0 0.0 0.0 0.0
+Cm 0.42 0.0 0.013 1.05e-3
+Hc 4.7e-4 0.0 1.05e-3 8.5e-5
+== ====== === ======= =======
+
+For a particular interaction pair, the user can also override the specified ``CombinationRule`` with custom parameters.
+The following overload would replace the parameters computed from a ``CombinationRule`` between ``Ow`` and ``Cm`` particle types.
+
+.. code:: cpp
+
+ interactions.add("Ow", "Cm", 0.42, 42e-6);
+
+To facilitate modular, reusable code, it is possible to combine multiple ``ParticleTypeInteractions`` objects.
+Assuming ``otherInteractions`` is defined, this can be done with ``interactions.merge(otherInteractions)``
+
+Define Molecules
+~~~~~~~~~~~~~~~~
+
+.. code:: cpp
+
+ Molecule water("Water");
+ Molecule methane("Methane");
+
+ water.addParticle(ParticleName("O"), Ow);
+ water.addParticle(ParticleName("H1"), Hw);
+ water.addParticle(ParticleName("H2"), Hw);
+
+ water.addExclusion("H1", "O");
+ water.addExclusion("H2", "O");
+
+ methane.addParticle(ParticleName("C"), Cm);
+ methane.addParticle(ParticleName("H1"), Hc);
+ methane.addParticle(ParticleName("H2"), Hc);
+ methane.addParticle(ParticleName("H3"), Hc);
+ methane.addParticle(ParticleName("H4"), Hc);
+
+ methane.addExclusion("H1", "C");
+ methane.addExclusion("H2", "C");
+ methane.addExclusion("H3", "C");
+ methane.addExclusion("H4", "C");
+
+We begin declaring molecules with their constituent particles.
+A string identifier must uniquely identify a specific particle within the molecule.
+It is also possible to define partial charges on each particle for the computation of Coulomb interactions.
+``water.addParticle(ParticleName("O"), Charge(-0.04), Ow);``
+
+Adding exclusions ensures that non-bonded interactions are only computed when necessary.
+For example, if two particles share a bond, the potential energy of the bond makes the non-bonded term negligible.
+Particle self-exclusions are enabled by default.
+We use the unique identifiers specified during ``addParticle()`` for this and the listed interactions later.
+
+Define Listed Interactions
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Within a molecule, one can define interactions such as bonds, angles and dihedrals between the constituent particles.
+NB-LIB provides concrete implementations of several commonly used 2, 3 and 4 center interactions.
+
+.. code:: cpp
+
+ HarmonicBondType ohHarmonicBond(1, 1);
+ HarmonicBondType hcHarmonicBond(2, 1);
+
+ DefaultAngle hohAngle(Degrees(120), 1);
+ DefaultAngle hchAngle(Degrees(109.5), 1);
+
+ //add harmonic bonds for water
+ water.addInteraction("O", "H1", ohHarmonicBond);
+ water.addInteraction("O", "H2", ohHarmonicBond);
+
+ // add the angle for water
+ water.addInteraction("H1", "O", "H2", hohAngle);
+
+ // add harmonic bonds for methane
+ methane.addInteraction("H1", "C", hcHarmonicBond);
+ methane.addInteraction("H2", "C", hcHarmonicBond);
+ methane.addInteraction("H3", "C", hcHarmonicBond);
+ methane.addInteraction("H4", "C", hhcHarmonicBondc);
+
+ // add the angles for methane
+ methane.addInteraction("H1", "C", "H2", hchAngle);
+ methane.addInteraction("H1", "C", "H3", hchAngle);
+ methane.addInteraction("H1", "C", "H4", hchAngle);
+ methane.addInteraction("H2", "C", "H3", hchAngle);
+ methane.addInteraction("H2", "C", "H4", hchAngle);
+ methane.addInteraction("H3", "C", "H4", hchAngle);
+
+Define Options for the Simulation and Non-Bonded Calculations
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code:: cpp
+
+ // Define a box for the simulation
+ Box box(6.05449);
+
+ // Define options for the non-bonded kernels
+ NBKernelOptions options;
+
+One can define the bounding box either with a single argument for a cube and 3 arguments to specify length, breadth and height separately.
+
+``NBKernelOptions`` contains a set of flags and configuration options for both hardware context and the relevant calculations for the simulation.
+The following table describes the possible options that can be set.
+
++----------------------+------+---------------------------------------+
+| Flag or Config | Type | Implications |
+| Option | | |
++======================+======+=======================================+
+| ``useGpu`` | Bool | Use GPU for non-bonded computations |
+| | ean | |
++----------------------+------+---------------------------------------+
+| ``numThreads`` | Inte | Number of CPU threads to use |
+| | ger | |
++----------------------+------+---------------------------------------+
+| ``nbnxmSimd`` | Enum | Kernel SIMD type |
+| | | (``SimdAuto``/``SimdNo``/``Simd4XM``/ |
+| | | ``Simd2XMM``) |
++----------------------+------+---------------------------------------+
+| ``ljCombination | Enum | Lennard-Jones combination rule |
+| Rule`` | | (``Geometric``/``LorentzBerthelot``) |
++----------------------+------+---------------------------------------+
+| ``useHalfLJOptimizat | Bool | Enable i-cluster half-LJ optimization |
+| ion`` | ean | |
++----------------------+------+---------------------------------------+
+| ``pairlistCutoff`` | Real | Specify pairlist and interaction |
+| | | cut-off |
++----------------------+------+---------------------------------------+
+| ``computeVirialAndEn | Bool | Enable energy computations |
+| ergy`` | ean | |
++----------------------+------+---------------------------------------+
+| ``coulombType`` | Enum | Coulomb interaction function |
+| | | (``Pme``/``Cutoff``/``ReactionField`` |
+| | | ) |
++----------------------+------+---------------------------------------+
+| ``useTabulatedEwaldC | Bool | Use tabulated PME grid correction |
+| orr`` | ean | instead of analytical |
++----------------------+------+---------------------------------------+
+| ``numIterations`` | Inte | Specify number of iterations for each |
+| | ger | kernel |
++----------------------+------+---------------------------------------+
+| ``cyclesPerPair`` | Bool | Enable printing cycles/pair instead |
+| | ean | of pairs/cycle |
++----------------------+------+---------------------------------------+
+| ``timestep`` | Real | Specify the time step |
++----------------------+------+---------------------------------------+
+
+Define Topology and Simulation State
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+We build the system topology using the ``TopologyBuilder`` class.
+We add the ``Molecule`` objects that we defined previously along with the ``ParticleTypesInteractions`` using its public functions.
+We get the actual ``Topology`` object complete with all exclusions, interaction maps and listed interaction data constructed based on the defined entities using the ``buildTopology()``\ function.
+
+.. code:: cpp
+
+ TopologyBuilder topologyBuilder;
+
+ // add molecules
+ topologyBuilder.addMolecule(water, 10);
+ topologyBuilder.addMolecule(methane, 10);
+
+ // add non-bonded interaction map
+ topologyBuilder.addParticleTypesInteractions(interactions);
+
+ Topology topology = topologyBuilder.buildTopology();
+
+We now have all we need to fully describe our system using the ``SimulationState`` object.
+This is built using the topology, the box, and the particle coordinates and velocities.
+This object serves as a snapshot of the system that can be used for analysis or to start simulations from known states.
+
+.. code:: cpp
+
+ SimulationState simulationState(coordinates, velocities, forces, box, topology);
+
+
+
+Writing the MD Loop
+~~~~~~~~~~~~~~~~~~~
+
+Now that we have fully described our system and the problem, we need two entities to write an MD loop.
+The first is the ``ForceCalculator`` and the second is an Integrator.
+NB-LIB comes with a ``LeapFrog`` integrator but it is also possible for users to write custom integrators.
+
+.. code:: cpp
+
+ // The force calculator contains all the data needed to compute forces
+ ForceCalculator forceCalculator(simulationState, options);
+
+ // Integration requires masses, positions, and forces
+ LeapFrog integrator(simulationState);
+
+ // Allocate a force buffer
+ gmx::ArrayRef<gmx::RVec> userForces(topology.numParticles());
+
+ // MD Loop
+ int numSteps = 100;
+
+ for (i = 0; i < numSteps; i++)
+ {
+ userForces = forceCalculator.compute();
+
+ // The forces are not automatically updated in case the user wants to add their own
+ std::copy(userForces.begin(), userForces.end(), begin(simulationState.forces()));
+
+ // Integrate with a time step of 1 fs
+ integrator.integrate(1.0);
+ }
+
+ return 0;
+ } // main
+
+.. _doxygen-ref-rvec: ../doxygen/html-lib/namespacegmx.xhtml#a139c1919a9680de4ad1450f42e37d33b
\ No newline at end of file
--- /dev/null
+.. _nblib:
+
+=========
+NBLIB API
+=========
+
+This documentation is part of the `GROMACS manual <http://manual.gromacs.org/current/>`_
+and describes the *nblib* API.
+
+
+.. toctree::
+ :maxdepth: 1
+ :caption: Documentation sections
+
+ guide-to-writing-MD-programs.rst
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