#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdlib/wholemoleculetransform.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcebuffers.h"
#include "gromacs/mdtypes/forcerec.h"
gmx_mtop_generate_local_top(top_global, top, inputrec.efep != FreeEnergyPerturbationType::No);
}
+ if (fr->wholeMoleculeTransform && usingDomDec)
+ {
+ fr->wholeMoleculeTransform->updateAtomOrder(cr->dd->globalAtomIndices, *cr->dd->ga2la);
+ }
+
if (vsite)
{
vsite->setVirtualSites(top->idef.il,
}
else
{
+ forcerec->bMolPBC = (!DOMAINDECOMP(commrec) || dd_bonded_molpbc(*commrec->dd, forcerec->pbcType));
+
+ // Check and set up PBC for Ewald surface corrections or orientation restraints
const bool useEwaldSurfaceCorrection =
(EEL_PME_EWALD(inputrec.coulombtype) && inputrec.epsilon_surface != 0);
const bool haveOrientationRestraints = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
- if (!DOMAINDECOMP(commrec))
+ const bool moleculesAreAlwaysWhole =
+ (DOMAINDECOMP(commrec) && dd_moleculesAreAlwaysWhole(*commrec->dd));
+ // WholeMoleculeTransform is only supported with a single PP rank
+ if (!moleculesAreAlwaysWhole && !havePPDomainDecomposition(commrec)
+ && (useEwaldSurfaceCorrection || haveOrientationRestraints))
{
- forcerec->bMolPBC = true;
-
- if (useEwaldSurfaceCorrection || haveOrientationRestraints)
- {
- forcerec->wholeMoleculeTransform =
- std::make_unique<gmx::WholeMoleculeTransform>(mtop, inputrec.pbcType);
- }
+ GMX_RELEASE_ASSERT(
+ !havePPDomainDecomposition(commrec),
+ "WholeMoleculesTransform only works when all atoms are in the same domain");
+ forcerec->wholeMoleculeTransform = std::make_unique<gmx::WholeMoleculeTransform>(
+ mtop, inputrec.pbcType, DOMAINDECOMP(commrec));
}
else
{
- forcerec->bMolPBC = dd_bonded_molpbc(*commrec->dd, forcerec->pbcType);
-
/* With Ewald surface correction it is useful to support e.g. running water
* in parallel with update groups.
* With orientation restraints there is no sensible use case supported with DD.
*/
- if ((useEwaldSurfaceCorrection && !dd_moleculesAreAlwaysWhole(*commrec->dd))
+ if ((useEwaldSurfaceCorrection
+ && !(DOMAINDECOMP(commrec) && dd_moleculesAreAlwaysWhole(*commrec->dd)))
|| haveOrientationRestraints)
{
gmx_fatal(FARGS,
if (useEwaldSurfaceCorrection)
{
- GMX_RELEASE_ASSERT(!DOMAINDECOMP(commrec) || dd_moleculesAreAlwaysWhole(*commrec->dd),
+ GMX_RELEASE_ASSERT(moleculesAreAlwaysWhole || forcerec->wholeMoleculeTransform,
"Molecules can not be broken by PBC with epsilon_surface > 0");
}
}
constrtestrunners_gpu.cpp
leapfrogtestrunners_gpu.cpp
settletestrunners_gpu.cpp
+ wholemoleculetransform.cpp
)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for the WholeMoleculeTransform class.
+ *
+ * \author berk Hess <hess@kth.se>
+ * \ingroup module_mdlib
+ */
+#include "gmxpre.h"
+
+#include "gromacs/mdlib/wholemoleculetransform.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/domdec/ga2la.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/topology.h"
+
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+//! The number of atoms for the test molecule
+constexpr int c_numAtoms = 4;
+//! The number of bonds, we use 2 bonds so we have one unbound atom
+constexpr int c_numBonds = 2;
+
+//! Returns a topology with a three atom molecule that is linearly connected
+std::unique_ptr<gmx_mtop_t> triAtomMoleculeSystem()
+{
+ gmx_moltype_t moltype;
+
+ moltype.atoms.nr = c_numAtoms;
+
+ for (int b = 0; b < c_numBonds; b++)
+ {
+ const int parameterType = -1; // value is not actually used
+ const std::array<int, 2> atomIndices = { b, b + 1 };
+ moltype.ilist[F_CONNBONDS].push_back(parameterType, atomIndices);
+ }
+
+ std::unique_ptr<gmx_mtop_t> mtop = std::make_unique<gmx_mtop_t>();
+
+ mtop->moltype.push_back(moltype);
+
+ gmx_molblock_t molblock;
+ molblock.type = 0;
+ molblock.nmol = 1;
+ mtop->molblock.push_back(molblock);
+ mtop->natoms = c_numAtoms;
+
+ return mtop;
+}
+
+
+//! Coordinates, broken over PBC
+const std::array<RVec, c_numAtoms> c_coords = {
+ { { 2.5, 0.5, 1.5 }, { 0.5, 0.5, 1.5 }, { 1.5, 0.5, 1.5 }, { 2.7, 0.5, 1.5 } }
+};
+
+//! A box that works with \p c_coords
+const matrix box = { { 3, 0, 0 }, { 0, 2, 0 }, { 0, 0, 2 } };
+
+TEST(WholeMoleculeTransform, MakesMoleculesWhole)
+{
+ const auto mtop = triAtomMoleculeSystem();
+
+ WholeMoleculeTransform wmt(*mtop, PbcType::Xyz, false);
+
+ wmt.updateForAtomPbcJumps(c_coords, box);
+
+ auto wholeCoords = wmt.wholeMoleculeCoordinates(c_coords, box);
+
+ for (int b = 0; b < c_numBonds; b++)
+ {
+ EXPECT_FLOAT_EQ(std::abs(wholeCoords[b][XX] - wholeCoords[b + 1][XX]), 1);
+ }
+}
+
+TEST(WholeMoleculeTransform, HandlesReordering)
+{
+ const auto mtop = triAtomMoleculeSystem();
+
+ WholeMoleculeTransform wmt(*mtop, PbcType::Xyz, true);
+
+ const std::array<int, c_numAtoms> reordering = { 2, 0, 3, 1 };
+
+ gmx_ga2la_t ga2la(c_numAtoms, c_numAtoms);
+ std::vector<RVec> coords;
+ for (int a = 0; a < c_numAtoms; a++)
+ {
+ ga2la.insert(reordering[a], { a, 0 });
+
+ coords.push_back(c_coords[reordering[a]]);
+ }
+
+ wmt.updateAtomOrder(reordering, ga2la);
+
+ wmt.updateForAtomPbcJumps(coords, box);
+
+ auto wholeCoords = wmt.wholeMoleculeCoordinates(coords, box);
+
+ for (int b = 0; b < c_numBonds; b++)
+ {
+ EXPECT_FLOAT_EQ(
+ std::abs(wholeCoords[ga2la.find(b)->la][XX] - wholeCoords[ga2la.find(b + 1)->la][XX]), 1);
+ }
+}
+
+} // namespace
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "wholemoleculetransform.h"
+#include "gromacs/domdec/ga2la.h"
#include "gromacs/topology/mtop_util.h"
namespace gmx
{
-WholeMoleculeTransform::WholeMoleculeTransform(const gmx_mtop_t& mtop, const PbcType pbcType) :
+WholeMoleculeTransform::WholeMoleculeTransform(const gmx_mtop_t& mtop,
+ const PbcType pbcType,
+ const bool useAtomReordering) :
pbcType_(pbcType)
{
gmx_localtop_t localTop(mtop.ffparams);
graph_ = mk_graph(localTop.idef, mtop.natoms);
wholeMoleculeCoordinates_.resize(mtop.natoms);
+
+ if (useAtomReordering)
+ {
+ // Store a copy of the global edges
+ globalEdgeAtomBegin_ = graph_.edgeAtomBegin;
+ graphGlobalAtomOrderEdges_ = graph_.edges;
+ // Reset the graph range to cover the whole system
+ graph_.edgeAtomBegin = 0;
+ graph_.edgeAtomEnd = graph_.shiftAtomEnd;
+
+ // Resize the edge color list for potential addition of non-connected atoms
+ graph_.edgeColor.resize(graph_.edgeAtomEnd);
+ }
+}
+
+void WholeMoleculeTransform::updateAtomOrder(ArrayRef<const int> globalAtomIndices, const gmx_ga2la_t& ga2la)
+{
+ GMX_RELEASE_ASSERT(!graphGlobalAtomOrderEdges_.empty(),
+ "We need the edges in the global atom order");
+
+ GMX_RELEASE_ASSERT(globalAtomIndices.ssize() == graph_.shiftAtomEnd,
+ "The number of indices should match the number of atoms we shift");
+
+ const int globalEdgeAtomEnd = globalEdgeAtomBegin_ + graphGlobalAtomOrderEdges_.size();
+ graph_.edges.clear();
+ for (const int globalAtomIndex : globalAtomIndices)
+ {
+ if (globalAtomIndex >= globalEdgeAtomBegin_ && globalAtomIndex < globalEdgeAtomEnd)
+ {
+ // Get the list of global atoms linked to this atom and add their local indices
+ const ArrayRef<const int> globalList =
+ graphGlobalAtomOrderEdges_[globalAtomIndex - globalEdgeAtomBegin_];
+ graph_.edges.pushBackListOfSize(globalList.size());
+ ArrayRef<int> lastList = graph_.edges.back();
+ std::transform(globalList.begin(), globalList.end(), lastList.begin(), [&ga2la](int i) -> int {
+ return ga2la.find(i)->la;
+ });
+ }
+ else
+ {
+ // The atom has no edges, push back an empty list
+ graph_.edges.pushBackListOfSize(0);
+ }
+ }
+
+ GMX_RELEASE_ASSERT(int(graph_.edges.size()) == graph_.shiftAtomEnd,
+ "We should have as many lists of edges as the system (shift) size");
}
void WholeMoleculeTransform::updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/utility/arrayref.h"
+class gmx_ga2la_t;
struct gmx_mtop_t;
enum class PbcType : int;
class WholeMoleculeTransform
{
public:
- /*! \brief Constructor */
- WholeMoleculeTransform(const gmx_mtop_t& mtop, PbcType pbcType);
+ /*! \brief Constructor
+ *
+ * \param[in] mtop The global topology use for getting the connections between atoms
+ * \param[in] pbcType The type of PBC
+ * \param[in] useAtomReordering Whether we will use atom reordering
+ */
+ WholeMoleculeTransform(const gmx_mtop_t& mtop, PbcType pbcType, bool useAtomReordering);
+
+ /*! \brief Changes the atom order to the one provided
+ *
+ * This method is called after domain repartitioning.
+ * The object should have been constructed with \p useAtomReordering set to \p true.
+ *
+ * \param[in] globalAtomIndices The global atom indices for the local atoms, size should be the system size
+ * \param[in] ga2la Global to local atom index lookup (the inverse of \p globalAtomIndices)
+ */
+ void updateAtomOrder(ArrayRef<const int> globalAtomIndices, const gmx_ga2la_t& ga2la);
/*! \brief Updates the graph when atoms have been shifted by periodic vectors */
void updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box);
PbcType pbcType_;
//! The graph
t_graph graph_;
+ //! The atom index at which graphGlobalAtomOrderEdges_ starts
+ int globalEdgeAtomBegin_;
+ //! The edges for the global atom order
+ ListOfLists<int> graphGlobalAtomOrderEdges_;
//! Buffer for storing coordinates for whole molecules
std::vector<RVec> wholeMoleculeCoordinates_;
};
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff