#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/pleasecite.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include "gromacs/awh/awh.h"
-#include "gromacs/fileio/enxio.h"
#include "gromacs/mdtypes/awh-params.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/compare.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
#define GMX_FILEIO_ENXIO_H
#include "gromacs/fileio/xdr_datatype.h"
-#include "gromacs/trajectory/energy.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
struct gmx_groups_t;
+struct t_energy;
+struct t_enxframe;
struct t_fileio;
struct t_inputrec;
class t_state;
int sval_alloc;
};
-
/* the energy file blocks. Each block contains a number of sub-blocks
of a single type that contain the actual data. */
-typedef struct t_enxblock{
+struct t_enxblock
+{
int id; /* block id, from the enx enums above */
int nsub; /* number of subblocks */
t_enxsubblock *sub; /* the subblocks */
int nsub_alloc; /* number of allocated subblocks */
-} t_enxblock;
-
-
-/* The frames that are read/written */
-struct t_enxframe {
- double t; /* Timestamp of this frame */
- gmx_int64_t step; /* MD step */
- gmx_int64_t nsteps; /* The number of steps between frames */
- double dt; /* The MD time step */
- int nsum; /* The number of terms for the sums in ener */
- int nre; /* Number of energies */
- int e_size; /* Size (in bytes) of energies */
- int e_alloc; /* Allocated size (in elements) of ener */
- t_energy *ener; /* The energies */
- int nblock; /* Number of following energy blocks */
- t_enxblock *block; /* The blocks */
- int nblock_alloc; /* The number of blocks allocated */
};
/* file handle */
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/statistics/statistics.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/binaryinformation.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/ifunc.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/random/tabulatednormaldistribution.h"
#include "gromacs/random/threefry.h"
#include "gromacs/random/uniformrealdistribution.h"
-#include "gromacs/trajectory/energy.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/ifunc.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include <stdio.h>
#include "gromacs/fileio/enxio.h"
-#include "gromacs/trajectory/energy.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/basedefinitions.h"
/* This is a running averaging structure ('energy bin') for use during mdrun. */
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/topology/mtop_util.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/basedefinitions.h"
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2018, 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.
# the research papers on the package. Check out http://www.gromacs.org.
gmx_add_libgromacs_sources(
+ energyframe.cpp
trajectoryframe.cpp
)
gmx_install_headers(
- energy.h
+ energyframe.h
trajectoryframe.h
)
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015, 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.
- */
-#ifndef GMX_TRAJECTORY_ENERGY_H
-#define GMX_TRAJECTORY_ENERGY_H
-
-#include "gromacs/utility/real.h"
-
-struct t_energy {
- //! The current energy.
- real e;
- //! The running average of the energy
- double eav;
- //! The sum of energies until now.
- double esum;
-};
-
-#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, 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 Implementions of related classes for tests that want to
+ * inspect energies produced by mdrun.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "energyframe.h"
+
+#include <map>
+#include <string>
+
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+EnergyFrame::EnergyFrame(const t_enxframe &enxframe,
+ const std::map<std::string, int> indicesOfEnergyFields)
+ : values_(), step_(enxframe.step), time_(enxframe.t)
+{
+ for (auto &index : indicesOfEnergyFields)
+ {
+ if (index.second >= enxframe.nre)
+ {
+ GMX_THROW(InternalError(formatString("Index %d for energy %s not present in energy frame with %d energies",
+ index.second, index.first.c_str(), enxframe.nre)));
+ }
+ values_[index.first] = enxframe.ener[index.second].e;
+ }
+}
+
+std::string EnergyFrame::frameName() const
+{
+ return formatString("Time %f Step %" GMX_PRId64, time_, step_);
+}
+
+const real &EnergyFrame::at(const std::string &name) const
+{
+ auto valueIterator = values_.find(name);
+ if (valueIterator == values_.end())
+ {
+ GMX_THROW(APIError("Cannot get energy value " + name + " unless previously registered when constructing EnergyFrameReader"));
+ }
+ return valueIterator->second;
+}
+
+EnergyFrame::MapConstIterator EnergyFrame::begin() const
+{
+ return values_.begin();
+}
+
+EnergyFrame::MapConstIterator EnergyFrame::end() const
+{
+ return values_.end();
+}
+
+EnergyFrame::MapConstIterator EnergyFrame::find(const std::string &key) const
+{
+ return values_.find(key);
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
+ */
+#ifndef GMX_TRAJECTORY_ENERGYFRAME_H
+#define GMX_TRAJECTORY_ENERGYFRAME_H
+
+#include <map>
+#include <string>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct t_enxblock;
+
+struct t_energy
+{
+ //! The current energy.
+ real e;
+ //! The running average of the energy
+ double eav;
+ //! The sum of energies until now.
+ double esum;
+};
+
+/* The frames that are read/written */
+struct t_enxframe
+{
+ double t; /* Timestamp of this frame */
+ gmx_int64_t step; /* MD step */
+ gmx_int64_t nsteps; /* The number of steps between frames */
+ double dt; /* The MD time step */
+ int nsum; /* The number of terms for the sums in ener */
+ int nre; /* Number of energies */
+ int e_size; /* Size (in bytes) of energies */
+ int e_alloc; /* Allocated size (in elements) of ener */
+ t_energy *ener; /* The energies */
+ int nblock; /* Number of following energy blocks */
+ t_enxblock *block; /* The blocks */
+ int nblock_alloc; /* The number of blocks allocated */
+};
+
+namespace gmx
+{
+
+/*! \internal
+ * \brief Contains the content of an .edr frame read by an EnergyFrameReader
+ *
+ * The interface of this class is intended to resemble a subset of std::map. */
+class EnergyFrame
+{
+ public:
+ //! Convenience type
+ using MapType = std::map<std::string, real>;
+ //! Convenience type
+ using MapConstIterator = MapType::const_iterator;
+ //! Constructor
+ EnergyFrame(const t_enxframe &enxframe,
+ const std::map<std::string, int> indicesOfEnergyFields);
+ /*! \brief Return string that helps users identify this frame, containing time and step number.
+ *
+ * \throws std::bad_alloc when out of memory */
+ std::string frameName() const;
+ /*! \brief Return the value read for energy \c name.
+ *
+ * \throws APIError if \c name was not registered with EnergyFileReader. */
+ const real &at(const std::string &name) const;
+ //! Return const interator to first element of values.
+ MapConstIterator begin() const;
+ //! Return const interator to past the end element of values.
+ MapConstIterator end() const;
+ //! Return a const interator to the element with \c key, or end() if not found.
+ MapConstIterator find(const std::string &key) const;
+ private:
+ //! Container for energy values, indexed by name
+ MapType values_;
+ //! Step number read from the .edr file frame
+ std::int64_t step_;
+ //! Time read from the .edr file frame
+ double time_;
+};
+
+} // namespace
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/veccompare.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/utility/compare.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
gmx_bool bRMSD, real ftol, real abstol)
sfree(frame->v);
sfree(frame->f);
}
+
+namespace gmx
+{
+
+TrajectoryFrame::TrajectoryFrame(const t_trxframe &frame)
+ : frame_(frame)
+{
+ // This would be nicer as an initializer, but once uncrustify is
+ // happy, Doxygen can't parse it.
+ box_ = {{{{0}}}};
+
+ if (!frame.bStep)
+ {
+ GMX_THROW(APIError("Cannot handle trajectory frame that lacks a step number"));
+ }
+ if (!frame.bTime)
+ {
+ GMX_THROW(APIError("Cannot handle trajectory frame that lacks a time"));
+ }
+ if (frame.bBox)
+ {
+ for (int d = 0; d < DIM; ++d)
+ {
+ for (int dd = 0; dd < DIM; ++dd)
+ {
+ box_[d][dd] = frame.box[d][dd];
+ }
+ }
+ }
+}
+
+std::string TrajectoryFrame::frameName() const
+{
+ return formatString("Time %f Step %" GMX_PRId64, frame_.time, frame_.step);
+}
+
+std::int64_t TrajectoryFrame::step() const
+{
+ return frame_.step;
+}
+
+double TrajectoryFrame::time() const
+{
+ return frame_.time;
+}
+
+int TrajectoryFrame::pbc() const
+{
+ return frame_.ePBC;
+}
+
+ArrayRef<const RVec> TrajectoryFrame::x() const
+{
+ return arrayRefFromArray(reinterpret_cast<RVec *>(frame_.x),
+ frame_.natoms);
+}
+
+ArrayRef<const RVec> TrajectoryFrame::v() const
+{
+ if (frame_.bV)
+ {
+ return arrayRefFromArray(reinterpret_cast<RVec *>(frame_.v),
+ frame_.natoms);
+ }
+ else
+ {
+ return EmptyArrayRef();
+ }
+}
+
+ArrayRef<const RVec> TrajectoryFrame::f() const
+{
+ if (frame_.bF)
+ {
+ return arrayRefFromArray(reinterpret_cast<RVec *>(frame_.f),
+ frame_.natoms);
+ }
+ else
+ {
+ return EmptyArrayRef();
+ }
+}
+
+bool TrajectoryFrame::hasBox() const
+{
+ return frame_.bBox;
+}
+
+const BoxMatrix &TrajectoryFrame::box() const
+{
+ return box_;
+}
+
+} // namespace gmx
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <array>
+
#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
void done_frame(t_trxframe *frame);
+namespace gmx
+{
+
+/*!\brief A 3x3 matrix data type useful for simulation boxes
+ *
+ * \todo Implement a full replacement for C-style real[DIM][DIM] */
+using BoxMatrix = std::array <std::array<real, DIM>, DIM>;
+
+/*! \internal
+ * \brief Contains a valid trajectory frame.
+ *
+ * Valid frames have a step and time, but need not have any particular
+ * other fields.
+ *
+ * \todo Eventually t_trxframe should be replaced by a class such as
+ * this. Currently we need to introduce BoxMatrix so that we can have
+ * a normal C++ getter that returns the contents of a box matrix,
+ * since you cannot use a real[DIM][DIM] as a function return type.
+ *
+ * \todo Consider a std::optional work-alike type for expressing that
+ * a field may or may not have content. */
+class TrajectoryFrame
+{
+ public:
+ /*! \brief Constructor
+ *
+ * \throws APIError If \c frame lacks either step or time.
+ */
+ explicit TrajectoryFrame(const t_trxframe &frame);
+ /*! \brief Return a string that helps users identify this frame, containing time and step number.
+ *
+ * \throws std::bad_alloc when out of memory */
+ std::string frameName() const;
+ //! Step number read from the trajectory file frame.
+ std::int64_t step() const;
+ //! Time read from the trajectory file frame.
+ double time() const;
+ //! The PBC characteristics of the box.
+ int pbc() const;
+ //! Get a view of position coordinates of the frame (which could be empty).
+ ArrayRef<const RVec> x() const;
+ //! Get a view of velocity coordinates of the frame (which could be empty).
+ ArrayRef<const RVec> v() const;
+ //! Get a view of force coordinates of the frame (which could be empty).
+ ArrayRef<const RVec> f() const;
+ //! Return whether the frame has a box.
+ bool hasBox() const;
+ //! Return a handle to the frame's box, which is all zero if the frame has no box.
+ const BoxMatrix &box() const;
+ // TODO make this private when updating trajectory comparison code
+ //! Handle to trajectory data
+ const t_trxframe &frame_;
+ private:
+ //! Box matrix data from the frame_.
+ BoxMatrix box_;
+};
+
+} // namespace gmx
+
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/fileio/enxio.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"
EnergyFrame
EnergyFrameReader::frame()
{
- EnergyFrame energyFrame;
-
if (!haveProbedForNextFrame_)
{
readNextFrame();
GMX_THROW(APIError("There is no next frame, so there should have been no attempt to use the data, e.g. by reacting to a call to readNextFrame()."));
}
- // The probe filled enxframe_ with new data, so now we use that data to fill energyFrame
- t_enxframe *enxframe = enxframeGuard_.get();
- energyFrame.time_ = enxframe->t;
- energyFrame.step_ = enxframe->step;
- for (auto &index : indicesOfEnergyFields_)
- {
- if (index.second >= enxframe->nre)
- {
- GMX_THROW(InternalError(formatString("Index %d for energy %s not present in energy frame with %d energies",
- index.second, index.first.c_str(), enxframe->nre)));
- }
- energyFrame.values_[index.first] = enxframe->ener[index.second].e;
- }
-
// Prepare for reading future frames
haveProbedForNextFrame_ = false;
nextFrameExists_ = false;
- return energyFrame;
-}
-
-// === EnergyFrame ===
-
-EnergyFrame::EnergyFrame() : values_(), step_(), time_() {};
-
-std::string EnergyFrame::getFrameName() const
-{
- return formatString("Time %f Step %" GMX_PRId64, time_, step_);
-}
-
-const real &EnergyFrame::at(const std::string &name) const
-{
- auto valueIterator = values_.find(name);
- if (valueIterator == values_.end())
- {
- GMX_THROW(APIError("Cannot get energy value " + name + " unless previously registered when constructing EnergyFrameReader"));
- }
- return valueIterator->second;
+ // The probe filled enxframe_ with new data, so now we use that data to fill energyFrame
+ return EnergyFrame(*enxframeGuard_.get(), indicesOfEnergyFields_);
}
void compareFrames(const std::pair<EnergyFrame, EnergyFrame> &frames,
auto &reference = frames.first;
auto &test = frames.second;
- for (auto referenceIt = reference.values_.begin(); referenceIt != reference.values_.end(); ++referenceIt)
+ for (auto referenceIt = reference.begin(); referenceIt != reference.end(); ++referenceIt)
{
- auto testIt = test.values_.find(referenceIt->first);
- if (testIt != test.values_.end())
+ auto testIt = test.find(referenceIt->first);
+ if (testIt != test.end())
{
auto energyFieldInReference = referenceIt->second;
auto energyFieldInTest = testIt->second;
EXPECT_REAL_EQ_TOL(energyFieldInReference, energyFieldInTest, tolerance)
- << referenceIt->first << " didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
+ << referenceIt->first << " didn't match between reference run " << reference.frameName() << " and test run " << test.frameName();
}
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018, 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.
namespace gmx
{
+
+class EnergyFrame;
+
namespace test
{
EnergyFrameReaderPtr openEnergyFileToReadFields(const std::string &filename,
const std::vector<std::string> &requiredEnergyFieldNames);
-class EnergyFrame;
-
//! Convenience smart pointer typedef
typedef unique_cptr<ener_file, done_ener_file> ener_file_ptr;
//! Helper function to free resources (NB free_enxframe only frees the contents, not the pointer itself)
void compareFrames(const std::pair<EnergyFrame, EnergyFrame> &frames,
FloatingPointTolerance tolerance);
-/*! \internal
- * \brief Contains the content of an .edr frame read by an EnergyFrameReader
- *
- * The interface of this class is intended to resemble a subset of std::map.
- *
- * Objects of this type are intended to be constructed by
- * EnergyFrameReader objects, and as such will always contain valid
- * data from an .edr file frame. */
-class EnergyFrame
-{
- public:
- /*! \brief Return string that helps users identify this frame, containing time and step number.
- *
- * \throws std::bad_alloc when out of memory */
- std::string getFrameName() const;
- /*! \brief Return the value read for energy \c name.
- *
- * \throws APIError if \c name was not registered with EnergyFileReader. */
- const real &at(const std::string &name) const;
- //! Constructor
- EnergyFrame();
- private:
- //! Container for energy values, indexed by name
- std::map<std::string, real> values_;
- //! Step number read from the .edr file frame
- std::int64_t step_;
- //! Time read from the .edr file frame
- double time_;
-
- friend class EnergyFrameReader;
- friend void compareFrames(const std::pair<EnergyFrame, EnergyFrame> &frames,
- FloatingPointTolerance tolerance);
-};
-
} // namespace
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/stringutil.h"
#include "energyreader.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/gpu_hw_info.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/stringutil.h"
while (energyReader->readNextFrame())
{
const EnergyFrame &frame = energyReader->frame();
- const std::string stepName = frame.getFrameName();
+ const std::string stepName = frame.frameName();
const real conservedEnergy = frame.at("Total Energy");
const real reciprocalEnergy = frame.at("Coul. recip.");
if (firstIteration)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, 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.
TrajectoryFrame
TrajectoryFrameReader::frame()
{
- TrajectoryFrame frame;
-
if (!haveProbedForNextFrame_)
{
readNextFrame();
nextFrameExists_ = false;
// The probe filled trxframeGuard_ with new data, so return it
- frame.frame_ = trxframeGuard_.get();
-
- if (!frame.frame_->bStep)
- {
- GMX_THROW(APIError("Cannot handle trajectory frame that lacks a step number"));
- }
-
- if (!frame.frame_->bTime)
- {
- GMX_THROW(APIError("Cannot handle trajectory frame that lacks a time"));
- }
-
- return frame;
-}
-
-// === TrajectoryFrame ===
-
-TrajectoryFrame::TrajectoryFrame() : frame_(nullptr) {};
-
-std::string TrajectoryFrame::getFrameName() const
-{
- GMX_RELEASE_ASSERT(frame_, "Cannot get name of invalid frame");
- return formatString("Time %f Step %" GMX_PRId64, frame_->time, frame_->step);
+ return TrajectoryFrame(*trxframeGuard_.get());
}
void compareFrames(const std::pair<TrajectoryFrame, TrajectoryFrame> &frames,
// NB We checked earlier for both frames that bStep and bTime are set
- EXPECT_EQ(reference.frame_->step, test.frame_->step)
- << "step didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
+ EXPECT_EQ(reference.frame_.step, test.frame_.step)
+ << "step didn't match between reference run " << reference.frameName() << " and test run " << test.frameName();
- EXPECT_EQ(reference.frame_->time, test.frame_->time)
- << "time didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
+ EXPECT_EQ(reference.frame_.time, test.frame_.time)
+ << "time didn't match between reference run " << reference.frameName() << " and test run " << test.frameName();
- for (int i = 0; i < reference.frame_->natoms && i < test.frame_->natoms; ++i)
+ for (int i = 0; i < reference.frame_.natoms && i < test.frame_.natoms; ++i)
{
for (int d = 0; d < DIM; ++d)
{
- if (reference.frame_->bX && test.frame_->bX)
+ if (reference.frame_.bX && test.frame_.bX)
{
- EXPECT_REAL_EQ_TOL(reference.frame_->x[i][d], test.frame_->x[i][d], tolerance)
- << " x[" << i << "][" << d <<"] didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
+ EXPECT_REAL_EQ_TOL(reference.frame_.x[i][d], test.frame_.x[i][d], tolerance)
+ << " x[" << i << "][" << d <<"] didn't match between reference run " << reference.frameName() << " and test run " << test.frameName();
}
- if (reference.frame_->bV && test.frame_->bV)
+ if (reference.frame_.bV && test.frame_.bV)
{
- EXPECT_REAL_EQ_TOL(reference.frame_->v[i][d], test.frame_->v[i][d], tolerance)
- << " v[" << i << "][" << d <<"] didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
+ EXPECT_REAL_EQ_TOL(reference.frame_.v[i][d], test.frame_.v[i][d], tolerance)
+ << " v[" << i << "][" << d <<"] didn't match between reference run " << reference.frameName() << " and test run " << test.frameName();
}
- if (reference.frame_->bF && test.frame_->bF)
+ if (reference.frame_.bF && test.frame_.bF)
{
- EXPECT_REAL_EQ_TOL(reference.frame_->f[i][d], test.frame_->f[i][d], tolerance)
- << " f[" << i << "][" << d <<"] didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
+ EXPECT_REAL_EQ_TOL(reference.frame_.f[i][d], test.frame_.f[i][d], tolerance)
+ << " f[" << i << "][" << d <<"] didn't match between reference run " << reference.frameName() << " and test run " << test.frameName();
}
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018, 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.
namespace gmx
{
-namespace test
-{
//! Forward declaration
class TrajectoryFrame;
+namespace test
+{
+
//! Convenience smart pointer typedef
typedef unique_cptr<gmx_output_env_t, output_env_done> oenv_ptr;
//! Convenience smart pointer typedef
void compareFrames(const std::pair<TrajectoryFrame, TrajectoryFrame> &frames,
FloatingPointTolerance tolerance);
-/*! \internal
- * \brief Contains the content of a trajectory frame read by an TrajectoryFrameReader
- *
- * Objects of this type are intended to be constructed by
- * TrajectoryFrameReader objects, and as such will always contain valid
- * data from an trajectory file frame. */
-class TrajectoryFrame
-{
- public:
- /*! \brief Return string that helps users identify this frame, containing time and step number.
- *
- * \throws std::bad_alloc when out of memory */
- std::string getFrameName() const;
- //! Constructor
- TrajectoryFrame();
-
- //! Handle to trajectory data
- t_trxframe *frame_;
-};
-
} // namespace
} // namespace
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff