--- /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.
+ *
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+ *
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+ */
+
+/*! \internal \file
+ * \brief
+ * SYCL implementation of coordinate layout conversion kernel and its wrapper
+ *
+ * \ingroup module_nbnxm
+ */
+#include "gmxpre.h"
+
+#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/gmxsycl.h"
+#include "gromacs/nbnxm/grid.h"
+#include "gromacs/nbnxm/nbnxm_gpu_buffer_ops_internal.h"
+
+#include "nbnxm_sycl_types.h"
+
+using cl::sycl::access::mode;
+using cl::sycl::access::target;
+
+namespace Nbnxm
+{
+
+/*! \brief SYCL kernel for transforming position coordinates from rvec to nbnxm layout.
+ *
+ * \param cgh SYCL's command group handler.
+ * \param[out] a_xq Coordinates buffer in nbnxm layout.
+ * \param[in] a_x Coordinates buffer.
+ * \param[in] a_atomIndex Atom index mapping.
+ * \param[in] a_numAtoms Array of number of atoms.
+ * \param[in] a_cellIndex Array of cell indices.
+ * \param[in] cellOffset First cell.
+ * \param[in] numAtomsPerCell Number of atoms per cell.
+ * \param[in] columnsOffset Index if the first column in the cell.
+ */
+static auto nbnxmKernelTransformXToXq(cl::sycl::handler& cgh,
+ DeviceAccessor<Float4, mode::read_write> a_xq,
+ DeviceAccessor<Float3, mode::read> a_x,
+ DeviceAccessor<int, mode::read> a_atomIndex,
+ DeviceAccessor<int, mode::read> a_numAtoms,
+ DeviceAccessor<int, mode::read> a_cellIndex,
+ int cellOffset,
+ int numAtomsPerCell,
+ int columnsOffset)
+{
+ cgh.require(a_xq);
+ cgh.require(a_x);
+ cgh.require(a_atomIndex);
+ cgh.require(a_numAtoms);
+ cgh.require(a_cellIndex);
+
+ return [=](cl::sycl::id<2> itemIdx) {
+ // Map cell-level parallelism to y component of block index.
+ const int cxy = itemIdx.get(1) + columnsOffset;
+
+ const int numAtoms = a_numAtoms[cxy];
+ const int offset = (cellOffset + a_cellIndex[cxy]) * numAtomsPerCell;
+
+ const int threadIndex = itemIdx.get(0);
+
+ // Perform layout conversion of each element.
+ if (threadIndex < numAtoms)
+ {
+ const float q = a_xq[threadIndex + offset][3];
+ const Float3 xNew = a_x[a_atomIndex[threadIndex + offset]];
+ a_xq[threadIndex + offset] = Float4(xNew[0], xNew[1], xNew[2], q);
+ }
+ };
+}
+
+// SYCL 1.2.1 requires providing a unique type for a kernel. Should not be needed for SYCL2020.
+class NbnxmKernelTransformXToXqName;
+
+void launchNbnxmKernelTransformXToXq(const Grid& grid,
+ NbnxmGpu* nb,
+ DeviceBuffer<Float3> d_x,
+ const DeviceStream& deviceStream,
+ unsigned int numColumnsMax,
+ int gridId)
+{
+ const unsigned int numColumns = grid.numColumns();
+ const unsigned int numAtomsMax = grid.numCellsColumnMax() * grid.numAtomsPerCell();
+ GMX_ASSERT(numColumns <= numColumnsMax, "Grid has more columns than allowed");
+
+ const cl::sycl::range<2> globalSize{ numAtomsMax, numColumns };
+ cl::sycl::queue q = deviceStream.stream();
+
+ q.submit([&](cl::sycl::handler& cgh) {
+ auto kernel = nbnxmKernelTransformXToXq(cgh,
+ nb->atdat->xq,
+ d_x,
+ nb->atomIndices,
+ nb->cxy_na,
+ nb->cxy_ind,
+ grid.cellOffset(),
+ grid.numAtomsPerCell(),
+ numColumnsMax * gridId);
+ cgh.parallel_for<NbnxmKernelTransformXToXqName>(globalSize, kernel);
+ });
+}
+
+} // namespace Nbnxm
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