diff --git a/CHANGELOG.rst b/CHANGELOG.rst index fc867054c1..3cc1a6fbe3 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -38,6 +38,9 @@ Change Log (`#1869 `__). * ``P`` property of ``hoomd.hpmc.compute.SDF`` (`#1869 `__). +* MPCD supports non-cubic collision cells, including both orthorhombic and triclinic cell shapes. + The cell size is controlled by the number of cells along each lattice vector that defines the + simulation box (`#1950 `__). *Changed* diff --git a/hoomd/mpcd/CellList.cc b/hoomd/mpcd/CellList.cc index 25efd67c28..e4e7b7a702 100644 --- a/hoomd/mpcd/CellList.cc +++ b/hoomd/mpcd/CellList.cc @@ -18,22 +18,53 @@ namespace hoomd { mpcd::CellList::CellList(std::shared_ptr sysdef, Scalar cell_size, bool shift) - : Compute(sysdef), m_mpcd_pdata(m_sysdef->getMPCDParticleData()), m_cell_size(cell_size), - m_cell_np_max(4), m_cell_np(m_exec_conf), m_cell_list(m_exec_conf), - m_embed_cell_ids(m_exec_conf), m_conditions(m_exec_conf), m_needs_compute_dim(true), - m_particles_sorted(false), m_virtual_change(false) + : Compute(sysdef), m_mpcd_pdata(m_sysdef->getMPCDParticleData()), m_cell_np_max(4), + m_cell_np(m_exec_conf), m_cell_list(m_exec_conf), m_embed_cell_ids(m_exec_conf), + m_conditions(m_exec_conf), m_needs_compute_dim(true), m_particles_sorted(false), + m_virtual_change(false) { assert(m_mpcd_pdata); m_exec_conf->msg->notice(5) << "Constructing MPCD CellList" << std::endl; - // by default, grid shifting is initialized to zeroes + setCellSize(cell_size); + m_origin_idx = make_int3(0, 0, 0); m_cell_dim = make_uint3(0, 0, 0); - m_global_cell_dim = make_uint3(0, 0, 0); m_enable_grid_shift = shift; m_grid_shift = make_scalar3(0.0, 0.0, 0.0); - m_max_grid_shift = 0.5 * m_cell_size; + + resetConditions(); + +#ifdef ENABLE_MPI + m_decomposition = m_pdata->getDomainDecomposition(); + m_num_extra = 0; + m_cover_box = m_pdata->getBox(); +#endif // ENABLE_MPI + + m_mpcd_pdata->getSortSignal().connect(this); + m_mpcd_pdata->getNumVirtualSignal().connect( + this); + m_pdata->getParticleSortSignal().connect(this); + m_pdata->getBoxChangeSignal().connect(this); + } + +mpcd::CellList::CellList(std::shared_ptr sysdef, + const uint3& global_cell_dim, + bool shift) + : Compute(sysdef), m_mpcd_pdata(m_sysdef->getMPCDParticleData()), m_cell_np_max(4), + m_cell_np(m_exec_conf), m_cell_list(m_exec_conf), m_embed_cell_ids(m_exec_conf), + m_conditions(m_exec_conf), m_needs_compute_dim(true), m_particles_sorted(false), + m_virtual_change(false) + { + assert(m_mpcd_pdata); + m_exec_conf->msg->notice(5) << "Constructing MPCD CellList" << std::endl; + + setGlobalDim(global_cell_dim); m_origin_idx = make_int3(0, 0, 0); + m_cell_dim = make_uint3(0, 0, 0); + + m_enable_grid_shift = shift; + m_grid_shift = make_scalar3(0.0, 0.0, 0.0); resetConditions(); @@ -140,55 +171,11 @@ void mpcd::CellList::reallocate() m_cell_list.resize(m_cell_list_indexer.getNumElements()); } -void mpcd::CellList::updateGlobalBox() - { - // triclinic boxes are not allowed - const BoxDim& global_box = m_pdata->getGlobalBox(); - if (global_box.getTiltFactorXY() != Scalar(0.0) || global_box.getTiltFactorXZ() != Scalar(0.0) - || global_box.getTiltFactorYZ() != Scalar(0.0)) - { - m_exec_conf->msg->error() << "mpcd: box must be orthorhombic" << std::endl; - throw std::runtime_error("Box must be orthorhombic"); - } - - // box must be evenly divisible by cell size - const Scalar3 L = global_box.getL(); - m_global_cell_dim = make_uint3((unsigned int)round(L.x / m_cell_size), - (unsigned int)round(L.y / m_cell_size), - (unsigned int)round(L.z / m_cell_size)); - if (m_sysdef->getNDimensions() == 2) - { - if (m_global_cell_dim.z > 1) - { - m_exec_conf->msg->error() - << "mpcd: In 2d simulations, box width must be smaller than cell size" << std::endl; - throw std::runtime_error("Lz bigger than cell size in 2D!"); - } - - // force to be only one cell along z in 2d - m_global_cell_dim.z = 1; - } - - const double eps = 1e-5; - if (fabs((double)L.x - m_global_cell_dim.x * (double)m_cell_size) > eps * m_cell_size - || fabs((double)L.y - m_global_cell_dim.y * (double)m_cell_size) > eps * m_cell_size - || (m_sysdef->getNDimensions() == 3 - && fabs((double)L.z - m_global_cell_dim.z * (double)m_cell_size) > eps * m_cell_size)) - { - m_exec_conf->msg->error() << "mpcd: Box size must be even multiple of cell size" - << std::endl; - throw std::runtime_error("MPCD cell size must evenly divide box"); - } - } - void mpcd::CellList::computeDimensions() { if (!m_needs_compute_dim) return; - // first update / validate the global box - updateGlobalBox(); - #ifdef ENABLE_MPI uchar3 communicating = make_uchar3(0, 0, 0); if (m_decomposition) @@ -202,34 +189,39 @@ void mpcd::CellList::computeDimensions() // Only do complicated sizing if some direction is being communicated if (communicating.x || communicating.y || communicating.z) { - // Global simulation box for absolute position referencing - const BoxDim& global_box = m_pdata->getGlobalBox(); - const Scalar3 global_lo = global_box.getLo(); - const Scalar3 global_L = global_box.getL(); - - // if global box is valid (no triclinic skew), then local box also has no skew, - // so assume orthorhombic in all subsequent calculations - const BoxDim& box = m_pdata->getBox(); + // fractional bounds of domain + const auto grid_pos = m_decomposition->getGridPos(); + Scalar3 fractional_lo = make_scalar3(m_decomposition->getCumulativeFraction(0, grid_pos.x), + m_decomposition->getCumulativeFraction(1, grid_pos.y), + m_decomposition->getCumulativeFraction(2, grid_pos.z)); + const Scalar3 fractional_hi + = make_scalar3(m_decomposition->getCumulativeFraction(0, grid_pos.x + 1), + m_decomposition->getCumulativeFraction(1, grid_pos.y + 1), + m_decomposition->getCumulativeFraction(2, grid_pos.z + 1)); // setup lo bin - const Scalar3 delta_lo = box.getLo() - global_lo; - int3 my_lo_bin = make_int3((int)std::floor((delta_lo.x - m_max_grid_shift) / m_cell_size), - (int)std::floor((delta_lo.y - m_max_grid_shift) / m_cell_size), - (int)std::floor((delta_lo.z - m_max_grid_shift) / m_cell_size)); + const Scalar3 fractional_lo_shifted_down = fractional_lo - m_max_grid_shift; + int3 my_lo_bin + = make_int3((int)std::floor(fractional_lo_shifted_down.x * m_global_cell_dim.x), + (int)std::floor(fractional_lo_shifted_down.y * m_global_cell_dim.y), + (int)std::floor(fractional_lo_shifted_down.z * m_global_cell_dim.z)); + const Scalar3 fractional_lo_shifted_up = fractional_lo + m_max_grid_shift; int3 lo_neigh_bin - = make_int3((int)std::ceil((delta_lo.x + m_max_grid_shift) / m_cell_size), - (int)std::ceil((delta_lo.y + m_max_grid_shift) / m_cell_size), - (int)std::ceil((delta_lo.z + m_max_grid_shift) / m_cell_size)); + = make_int3((int)std::ceil(fractional_lo_shifted_up.x * m_global_cell_dim.x), + (int)std::ceil(fractional_lo_shifted_up.y * m_global_cell_dim.y), + (int)std::ceil(fractional_lo_shifted_up.z * m_global_cell_dim.z)); // setup hi bin - const Scalar3 delta_hi = box.getHi() - global_lo; - int3 my_hi_bin = make_int3((int)std::ceil((delta_hi.x + m_max_grid_shift) / m_cell_size), - (int)std::ceil((delta_hi.y + m_max_grid_shift) / m_cell_size), - (int)std::ceil((delta_hi.z + m_max_grid_shift) / m_cell_size)); + const Scalar3 fractional_hi_shifted_up = fractional_hi + m_max_grid_shift; + int3 my_hi_bin + = make_int3((int)std::ceil(fractional_hi_shifted_up.x * m_global_cell_dim.x), + (int)std::ceil(fractional_hi_shifted_up.y * m_global_cell_dim.y), + (int)std::ceil(fractional_hi_shifted_up.z * m_global_cell_dim.z)); + const Scalar3 fractional_hi_shifted_down = fractional_hi - m_max_grid_shift; int3 hi_neigh_bin - = make_int3((int)std::floor((delta_hi.x - m_max_grid_shift) / m_cell_size), - (int)std::floor((delta_hi.y - m_max_grid_shift) / m_cell_size), - (int)std::floor((delta_hi.z - m_max_grid_shift) / m_cell_size)); + = make_int3((int)std::floor(fractional_hi_shifted_down.x * m_global_cell_dim.x), + (int)std::floor(fractional_hi_shifted_down.y * m_global_cell_dim.y), + (int)std::floor(fractional_hi_shifted_down.z * m_global_cell_dim.z)); // initially size the grid assuming one rank in each direction, and then resize based on // communication @@ -238,9 +230,10 @@ void mpcd::CellList::computeDimensions() std::fill(m_num_comm.begin(), m_num_comm.end(), 0); // Compute size of the box with diffusion layer - Scalar3 cover_lo = box.getLo(); - Scalar3 cover_hi = box.getHi(); - uchar3 cover_periodic = box.getPeriodic(); + const BoxDim& global_box = m_pdata->getGlobalBox(); + uchar3 cover_periodic = global_box.getPeriodic(); + Scalar3 fractional_cover_lo = fractional_lo; + Scalar3 fractional_cover_hi = fractional_hi; if (communicating.x) { @@ -255,9 +248,9 @@ void mpcd::CellList::computeDimensions() = lo_neigh_bin.x - my_lo_bin.x + m_num_extra; // "safe" size of the diffusion layer - cover_lo.x = m_origin_idx.x * m_cell_size + m_max_grid_shift - 0.5 * global_L.x; - cover_hi.x = (m_origin_idx.x + m_cell_dim.x) * m_cell_size - m_max_grid_shift - - 0.5 * global_L.x; + fractional_cover_lo.x = m_global_cell_dim_inv.x * m_origin_idx.x + m_max_grid_shift.x; + fractional_cover_hi.x + = m_global_cell_dim_inv.x * (m_origin_idx.x + m_cell_dim.x) - m_max_grid_shift.x; cover_periodic.x = 0; } @@ -271,9 +264,9 @@ void mpcd::CellList::computeDimensions() m_num_comm[static_cast(mpcd::detail::face::south)] = lo_neigh_bin.y - my_lo_bin.y + m_num_extra; - cover_lo.y = m_origin_idx.y * m_cell_size + m_max_grid_shift - 0.5 * global_L.y; - cover_hi.y = (m_origin_idx.y + m_cell_dim.y) * m_cell_size - m_max_grid_shift - - 0.5 * global_L.y; + fractional_cover_lo.y = m_global_cell_dim_inv.y * m_origin_idx.y + m_max_grid_shift.y; + fractional_cover_hi.y + = m_global_cell_dim_inv.y * (m_origin_idx.y + m_cell_dim.y) - m_max_grid_shift.y; cover_periodic.y = 0; } @@ -287,16 +280,22 @@ void mpcd::CellList::computeDimensions() m_num_comm[static_cast(mpcd::detail::face::down)] = lo_neigh_bin.z - my_lo_bin.z + m_num_extra; - cover_lo.z = m_origin_idx.z * m_cell_size + m_max_grid_shift - 0.5 * global_L.z; - cover_hi.z = (m_origin_idx.z + m_cell_dim.z) * m_cell_size - m_max_grid_shift - - 0.5 * global_L.z; + fractional_cover_lo.z = m_global_cell_dim_inv.z * m_origin_idx.z + m_max_grid_shift.z; + fractional_cover_hi.z + = m_global_cell_dim_inv.z * (m_origin_idx.z + m_cell_dim.z) - m_max_grid_shift.z; cover_periodic.z = 0; } // set the box covered by this cell list - m_cover_box = BoxDim(cover_lo, cover_hi, cover_periodic); - - checkDomainBoundaries(); + // this requires us to reduce the box back to equivalent cube lengths + const Scalar3 global_lo = global_box.getLo(); + const Scalar3 global_L = global_box.getL(); + m_cover_box = BoxDim(global_lo + fractional_cover_lo * global_L, + global_lo + fractional_cover_hi * global_L, + cover_periodic); + m_cover_box.setTiltFactors(global_box.getTiltFactorXY(), + global_box.getTiltFactorXZ(), + global_box.getTiltFactorYZ()); } else #endif // ENABLE_MPI @@ -319,184 +318,6 @@ void mpcd::CellList::computeDimensions() } #ifdef ENABLE_MPI -void mpcd::CellList::checkDomainBoundaries() - { - if (!m_decomposition) - return; - - MPI_Comm mpi_comm = m_exec_conf->getMPICommunicator(); - - for (unsigned int dir = 0; dir < m_num_comm.size(); ++dir) - { - mpcd::detail::face d = static_cast(dir); - if (!isCommunicating(d)) - continue; - - // receive in the opposite direction from which we send - unsigned int send_neighbor = m_decomposition->getNeighborRank(dir); - unsigned int recv_neighbor; - if (dir % 2 == 0) - recv_neighbor = m_decomposition->getNeighborRank(dir + 1); - else - recv_neighbor = m_decomposition->getNeighborRank(dir - 1); - - // first make sure each dimension is sending and receiving the same size data - MPI_Request reqs[2]; - MPI_Status status[2]; - - // check that the number received is the same as that being sent from neighbor - unsigned int n_send = m_num_comm[dir]; - unsigned int n_expect_recv; - if (dir % 2 == 0) - n_expect_recv = m_num_comm[dir + 1]; - else - n_expect_recv = m_num_comm[dir - 1]; - - unsigned int n_recv; - MPI_Isend(&n_send, 1, MPI_UNSIGNED, send_neighbor, 0, mpi_comm, &reqs[0]); - MPI_Irecv(&n_recv, 1, MPI_UNSIGNED, recv_neighbor, 0, mpi_comm, &reqs[1]); - MPI_Waitall(2, reqs, status); - - // check if any rank errored out - unsigned int recv_error = 0; - if (n_expect_recv != n_recv) - { - recv_error = 1; - } - unsigned int any_error = 0; - MPI_Allreduce(&recv_error, &any_error, 1, MPI_UNSIGNED, MPI_SUM, mpi_comm); - if (any_error) - { - if (recv_error) - { - m_exec_conf->msg->error() << "mpcd: expected to communicate " << n_expect_recv - << " cells, but only receiving " << n_recv << std::endl; - } - throw std::runtime_error("Error setting up MPCD cell list"); - } - - // check that the same cell ids are communicated - std::vector send_cells(n_send), recv_cells(n_recv); - for (unsigned int i = 0; i < n_send; ++i) - { - if (d == mpcd::detail::face::east) - { - send_cells[i] = m_origin_idx.x + m_cell_dim.x - m_num_extra - n_send + i; - } - else if (d == mpcd::detail::face::west) - { - send_cells[i] = m_origin_idx.x + i; - } - else if (d == mpcd::detail::face::north) - { - send_cells[i] = m_origin_idx.y + m_cell_dim.y - m_num_extra - n_send + i; - } - else if (d == mpcd::detail::face::south) - { - send_cells[i] = m_origin_idx.y + i; - } - else if (d == mpcd::detail::face::up) - { - send_cells[i] = m_origin_idx.z + m_cell_dim.z - m_num_extra - n_send + i; - } - else if (d == mpcd::detail::face::down) - { - send_cells[i] = m_origin_idx.z + i; - } - } - - MPI_Isend(&send_cells[0], n_send, MPI_INT, send_neighbor, 1, mpi_comm, &reqs[0]); - MPI_Irecv(&recv_cells[0], n_recv, MPI_INT, recv_neighbor, 1, mpi_comm, &reqs[1]); - MPI_Waitall(2, reqs, status); - - unsigned int overlap_error = 0; - std::array err_pair {0, 0}; - for (unsigned int i = 0; i < n_recv && !overlap_error; ++i) - { - // wrap the received cell back into the global box - // only two of the entries will be valid, the others are dummies - int3 recv_cell = make_int3(0, 0, 0); - if (d == mpcd::detail::face::east || d == mpcd::detail::face::west) - { - recv_cell.x = recv_cells[i]; - } - else if (d == mpcd::detail::face::north || d == mpcd::detail::face::south) - { - recv_cell.y = recv_cells[i]; - } - else if (d == mpcd::detail::face::up || d == mpcd::detail::face::down) - { - recv_cell.z = recv_cells[i]; - } - recv_cell = wrapGlobalCell(recv_cell); - - // compute the expected cell to receive, also wrapped - int3 expect_recv_cell = make_int3(0, 0, 0); - if (d == mpcd::detail::face::east) - { - expect_recv_cell.x = m_origin_idx.x + i; - } - else if (d == mpcd::detail::face::west) - { - expect_recv_cell.x = m_origin_idx.x + m_cell_dim.x - m_num_extra - n_recv + i; - } - else if (d == mpcd::detail::face::north) - { - expect_recv_cell.y = m_origin_idx.y + i; - } - else if (d == mpcd::detail::face::south) - { - expect_recv_cell.y = m_origin_idx.y + m_cell_dim.y - m_num_extra - n_recv + i; - } - else if (d == mpcd::detail::face::up) - { - expect_recv_cell.z = m_origin_idx.z + i; - } - else if (d == mpcd::detail::face::down) - { - expect_recv_cell.z = m_origin_idx.z + m_cell_dim.z - m_num_extra - n_recv + i; - } - expect_recv_cell = wrapGlobalCell(expect_recv_cell); - - if (recv_cell.x != expect_recv_cell.x || recv_cell.y != expect_recv_cell.y - || recv_cell.z != expect_recv_cell.z) - { - overlap_error = i; - if (d == mpcd::detail::face::east || d == mpcd::detail::face::west) - { - err_pair[0] = recv_cell.x; - err_pair[1] = expect_recv_cell.x; - } - else if (d == mpcd::detail::face::north || d == mpcd::detail::face::south) - { - err_pair[0] = recv_cell.y; - err_pair[1] = expect_recv_cell.y; - } - else if (d == mpcd::detail::face::up || d == mpcd::detail::face::down) - { - err_pair[0] = recv_cell.z; - err_pair[1] = expect_recv_cell.z; - } - } - } - - // check if anyone reported an error, then race to see who gets to write it out - any_error = 0; - MPI_Allreduce(&overlap_error, &any_error, 1, MPI_UNSIGNED, MPI_SUM, mpi_comm); - if (any_error) - { - if (overlap_error) - { - m_exec_conf->msg->error() - << "mpcd: communication grid does not overlap. " << "Expected to receive cell " - << err_pair[1] << " from rank " << recv_neighbor << ", but got cell " - << err_pair[0] << "." << std::endl; - } - throw std::runtime_error("Error setting up MPCD cell list"); - } - } - } - /*! * \param dir Direction of communication * \returns True if communication is occurring along \a dir @@ -579,7 +400,7 @@ void mpcd::CellList::buildCellList() n_global_cells.z += 2 * m_num_extra; #endif // ENABLE_MPI - const Scalar3 global_lo = m_pdata->getGlobalBox().getLo(); + const BoxDim& global_box = m_pdata->getGlobalBox(); for (unsigned int cur_p = 0; cur_p < N_tot; ++cur_p) { @@ -600,11 +421,11 @@ void mpcd::CellList::buildCellList() continue; } - // bin particle assuming orthorhombic box (already validated) - const Scalar3 delta = (pos_i - m_grid_shift) - global_lo; - int3 global_bin = make_int3((int)std::floor(delta.x / m_cell_size), - (int)std::floor(delta.y / m_cell_size), - (int)std::floor(delta.z / m_cell_size)); + // bin particle + const Scalar3 fractional_pos_i = global_box.makeFraction(pos_i) - m_grid_shift; + int3 global_bin = make_int3((int)std::floor(fractional_pos_i.x * m_global_cell_dim.x), + (int)std::floor(fractional_pos_i.y * m_global_cell_dim.y), + (int)std::floor(fractional_pos_i.z * m_global_cell_dim.z)); // wrap cell back through the boundaries (grid shifting may send +/- 1 outside of range) // this is done using periodic from the "local" box, since this will be periodic @@ -635,6 +456,28 @@ void mpcd::CellList::buildCellList() int3 bin = make_int3(global_bin.x - m_origin_idx.x, global_bin.y - m_origin_idx.y, global_bin.z - m_origin_idx.z); + // these checks guard against round-off errors with domain decomposition + if (!periodic.x) + { + if (bin.x == -1) + bin.x = 0; + else if (bin.x == (int)m_cell_dim.x) + bin.x = m_cell_dim.x - 1; + } + if (!periodic.y) + { + if (bin.y == -1) + bin.y = 0; + else if (bin.y == (int)m_cell_dim.y) + bin.y = m_cell_dim.y - 1; + } + if (!periodic.z) + { + if (bin.z == -1) + bin.z = 0; + else if (bin.z == (int)m_cell_dim.z) + bin.z = m_cell_dim.z - 1; + } // validate and make sure no particles blew out of the box if ((bin.x < 0 || bin.x >= (int)m_cell_dim.x) || (bin.y < 0 || bin.y >= (int)m_cell_dim.y) @@ -688,15 +531,16 @@ void mpcd::CellList::sort(uint64_t timestep, return; // if mapping is not valid, signal that we need to force a recompute next time - // that the cell list is needed. We don't call forceCompute() directly because this always - // runs compute(), and we just want to defer to the next compute() call. + // that the cell list is needed. We don't call forceCompute() directly because this + // always runs compute(), and we just want to defer to the next compute() call. if (rorder.isNull()) { m_force_compute = true; return; } - // iterate through particles in cell list, and update their indexes using reverse mapping + // iterate through particles in cell list, and update their indexes using reverse + // mapping ArrayHandle h_rorder(rorder, access_location::host, access_mode::read); ArrayHandle h_cell_np(m_cell_np, access_location::host, access_mode::read); ArrayHandle h_cell_list(m_cell_list, @@ -730,9 +574,7 @@ bool mpcd::CellList::needsEmbedMigrate(uint64_t timestep) // ensure that the cell list has been sized first computeDimensions(); - // coverage box dimensions, assuming orthorhombic - const Scalar3 lo = m_cover_box.getLo(); - const Scalar3 hi = m_cover_box.getHi(); + // coverage box dimensions const uchar3 periodic = m_cover_box.getPeriodic(); const unsigned int ndim = m_sysdef->getNDimensions(); @@ -750,10 +592,11 @@ bool mpcd::CellList::needsEmbedMigrate(uint64_t timestep) const unsigned int idx = h_group.data[i]; const Scalar4 postype = h_pos.data[idx]; const Scalar3 pos = make_scalar3(postype.x, postype.y, postype.z); - - if ((!periodic.x && (pos.x >= hi.x || pos.x < lo.x)) - || (!periodic.y && (pos.y >= hi.y || pos.y < lo.y)) - || (!periodic.z && ndim == 3 && (pos.z >= hi.z || pos.z < lo.z))) + const Scalar3 fractional_pos = m_cover_box.makeFraction(pos); + if ((!periodic.x && (fractional_pos.x >= Scalar(1.0) || fractional_pos.x < Scalar(0.0))) + || (!periodic.y && (fractional_pos.y >= Scalar(1.0) || fractional_pos.y < Scalar(0.0))) + || (!periodic.z && ndim == 3 + && (fractional_pos.z >= Scalar(1.0) || fractional_pos.z < Scalar(0.0)))) { migrate = 1; } @@ -802,6 +645,7 @@ bool mpcd::CellList::checkConditions() { unsigned int n = conditions.z - 1; Scalar4 pos_empty_i; + std::string msg; if (n < m_mpcd_pdata->getN() + m_mpcd_pdata->getNVirtual()) { ArrayHandle h_pos(m_mpcd_pdata->getPositions(), @@ -809,11 +653,9 @@ bool mpcd::CellList::checkConditions() access_mode::read); pos_empty_i = h_pos.data[n]; if (n < m_mpcd_pdata->getN()) - m_exec_conf->msg->errorAllRanks() - << "MPCD particle is no longer in the simulation box" << std::endl; + msg = "MPCD particle is no longer in the simulation box"; else - m_exec_conf->msg->errorAllRanks() - << "MPCD virtual particle is no longer in the simulation box" << std::endl; + msg = "MPCD virtual particle is no longer in the simulation box"; } else { @@ -827,27 +669,17 @@ bool mpcd::CellList::checkConditions() = h_pos_embed .data[h_embed_member_idx .data[n - (m_mpcd_pdata->getN() + m_mpcd_pdata->getNVirtual())]]; - m_exec_conf->msg->errorAllRanks() - << "Embedded particle is no longer in the simulation box" << std::endl; + msg = "Embedded particle is no longer in the simulation box"; } Scalar3 pos = make_scalar3(pos_empty_i.x, pos_empty_i.y, pos_empty_i.z); m_exec_conf->msg->errorAllRanks() + << msg << std::endl << "Cartesian coordinates: " << std::endl << "x: " << pos.x << " y: " << pos.y << " z: " << pos.z << std::endl << "Grid shift: " << std::endl << "x: " << m_grid_shift.x << " y: " << m_grid_shift.y << " z: " << m_grid_shift.z << std::endl; - - const BoxDim cover_box = getCoverageBox(); - Scalar3 lo = cover_box.getLo(); - Scalar3 hi = cover_box.getHi(); - uchar3 periodic = cover_box.getPeriodic(); - m_exec_conf->msg->errorAllRanks() - << "Covered box lo: (" << lo.x << ", " << lo.y << ", " << lo.z << ")" << std::endl - << " hi: (" << hi.x << ", " << hi.y << ", " << hi.z << ")" << std::endl - << " periodic: (" << ((periodic.x) ? "1" : "0") << " " - << ((periodic.y) ? "1" : "0") << " " << ((periodic.z) ? "1" : "0") << ")" << std::endl; throw std::runtime_error("Error computing cell list"); } @@ -873,6 +705,8 @@ void mpcd::CellList::drawGridShift(uint64_t timestep) { if (m_enable_grid_shift) { + computeDimensions(); + uint16_t seed = m_sysdef->getSeed(); // PRNG using seed and timestep as seeds @@ -880,29 +714,35 @@ void mpcd::CellList::drawGridShift(uint64_t timestep) hoomd::Counter()); // draw shift variables from uniform distribution - hoomd::UniformDistribution uniform(-m_max_grid_shift, m_max_grid_shift); - Scalar3 shift; - shift.x = uniform(rng); - shift.y = uniform(rng); - shift.z = (m_sysdef->getNDimensions() == 3) ? uniform(rng) : Scalar(0.0); + hoomd::UniformDistribution uniform(Scalar(-0.5), Scalar(0.5)); + Scalar3 shift = make_scalar3( + uniform(rng) * m_global_cell_dim_inv.x, + uniform(rng) * m_global_cell_dim_inv.y, + (m_sysdef->getNDimensions() == 3) ? uniform(rng) * m_global_cell_dim_inv.z : 0); setGridShift(shift); } } -void mpcd::CellList::getCellStatistics() const +void mpcd::CellList::setGlobalDim(const uint3& global_cell_dim) { - unsigned int min_np(0xffffffff), max_np(0); - ArrayHandle h_cell_np(m_cell_np, access_location::host, access_mode::read); - for (unsigned int cur_cell = 0; cur_cell < m_cell_indexer.getNumElements(); ++cur_cell) + if (global_cell_dim.x == 0 || global_cell_dim.y == 0) { - const unsigned int np = h_cell_np.data[cur_cell]; - if (np < min_np) - min_np = np; - if (np > max_np) - max_np = np; + throw std::runtime_error("Global cell dimensions must be at least 1"); } - m_exec_conf->msg->notice(2) << "MPCD cell list stats:" << std::endl; - m_exec_conf->msg->notice(2) << "Min: " << min_np << " Max: " << max_np << std::endl; + + m_global_cell_dim = global_cell_dim; + if (m_sysdef->getNDimensions() == 2) + { + m_global_cell_dim.z = 1; + } + + m_global_cell_dim_inv = make_scalar3(Scalar(1.0) / global_cell_dim.x, + Scalar(1.0) / global_cell_dim.y, + Scalar(1.0) / global_cell_dim.z); + + m_max_grid_shift = Scalar(0.5) * m_global_cell_dim_inv; + + m_needs_compute_dim = true; } /*! @@ -912,8 +752,10 @@ void mpcd::CellList::getCellStatistics() const * \warning The returned cell index may lie outside the local grid. It is the * caller's responsibility to check that the index is valid. */ -const int3 mpcd::CellList::getLocalCell(const int3& global) const +const int3 mpcd::CellList::getLocalCell(const int3& global) { + computeDimensions(); + int3 local = make_int3(global.x - m_origin_idx.x, global.y - m_origin_idx.y, global.z - m_origin_idx.z); @@ -928,21 +770,65 @@ const int3 mpcd::CellList::getLocalCell(const int3& global) const * Local cell coordinates are wrapped around the global box so that a valid global * index is computed. */ -const int3 mpcd::CellList::getGlobalCell(const int3& local) const +const int3 mpcd::CellList::getGlobalCell(const int3& local) { + computeDimensions(); + int3 global = make_int3(local.x + m_origin_idx.x, local.y + m_origin_idx.y, local.z + m_origin_idx.z); return wrapGlobalCell(global); } +Scalar3 mpcd::CellList::getCellSize() + { + computeDimensions(); + + const BoxDim& global_box = m_pdata->getGlobalBox(); + const Scalar3 L = global_box.getL(); + return make_scalar3(L.x * m_global_cell_dim_inv.x, + L.y * m_global_cell_dim_inv.y, + L.z * m_global_cell_dim_inv.z); + } + +/*! + * \param cell_size Grid spacing + * \note Calling forces a resize of the cell list on the next update + */ +void mpcd::CellList::setCellSize(Scalar cell_size) + { + const BoxDim& global_box = m_pdata->getGlobalBox(); + const Scalar3 L = global_box.getL(); + uint3 global_cell_dim = make_uint3((unsigned int)round(L.x / cell_size), + (unsigned int)round(L.y / cell_size), + (unsigned int)round(L.z / cell_size)); + if (m_sysdef->getNDimensions() == 2) + { + global_cell_dim.z = 1; + } + + // check that box is a multiple of cell size + const double eps = 1e-5; + if (fabs((double)L.x - global_cell_dim.x * (double)cell_size) > eps * cell_size + || fabs((double)L.y - global_cell_dim.y * (double)cell_size) > eps * cell_size + || (m_sysdef->getNDimensions() == 3 + && fabs((double)L.z - global_cell_dim.z * (double)cell_size) > eps * cell_size)) + { + throw std::runtime_error("MPCD cell size must evenly divide box"); + } + + setGlobalDim(global_cell_dim); + } + /*! * \param cell Cell coordinates to wrap back into the global box * * \warning Only up to one global box size is wrapped. This method is intended * to be used for wrapping cells off by only one or two from the global boundary. */ -const int3 mpcd::CellList::wrapGlobalCell(const int3& cell) const +const int3 mpcd::CellList::wrapGlobalCell(const int3& cell) { + computeDimensions(); + int3 wrap = cell; if (wrap.x >= (int)m_global_cell_dim.x) @@ -971,7 +857,19 @@ void export_CellList(pybind11::module& m) { pybind11::class_>(m, "CellList") .def(pybind11::init, Scalar, bool>()) - .def_property("cell_size", &mpcd::CellList::getCellSize, &mpcd::CellList::setCellSize) + .def_property( + "num_cells", + [](const mpcd::CellList& cl) + { + const auto num_cells = cl.getGlobalDim(); + return pybind11::make_tuple(num_cells.x, num_cells.y, num_cells.z); + }, + [](mpcd::CellList& cl, const pybind11::tuple& num_cells) + { + cl.setGlobalDim(make_uint3(pybind11::cast(num_cells[0]), + pybind11::cast(num_cells[1]), + pybind11::cast(num_cells[2]))); + }) .def_property("shift", &mpcd::CellList::isGridShifting, &mpcd::CellList::enableGridShifting); diff --git a/hoomd/mpcd/CellList.h b/hoomd/mpcd/CellList.h index e76ea2ca2b..2ffa165f9e 100644 --- a/hoomd/mpcd/CellList.h +++ b/hoomd/mpcd/CellList.h @@ -33,9 +33,12 @@ namespace mpcd class PYBIND11_EXPORT CellList : public Compute { public: - //! Constructor + //! Constructor by size (deprecated) CellList(std::shared_ptr sysdef, Scalar cell_size, bool shift); + //! Constructor by dimension + CellList(std::shared_ptr sysdef, const uint3& global_cell_dim, bool shift); + //! Destructor virtual ~CellList(); @@ -93,19 +96,21 @@ class PYBIND11_EXPORT CellList : public Compute return m_global_cell_dim; } + void setGlobalDim(const uint3& global_cell_dim); + const int3& getOriginIndex() const { return m_origin_idx; } //! Obtain the local cell index corresponding to a global cell - const int3 getLocalCell(const int3& global) const; + const int3 getLocalCell(const int3& global); //! Obtain the global cell corresponding to local cell - const int3 getGlobalCell(const int3& local) const; + const int3 getGlobalCell(const int3& local); //! Wrap a cell into a global cell - const int3 wrapGlobalCell(const int3& cell) const; + const int3 wrapGlobalCell(const int3& cell); //! Get the maximum number of particles in a cell const unsigned int getNmax() const @@ -113,23 +118,11 @@ class PYBIND11_EXPORT CellList : public Compute return m_cell_np_max; } - //! Set the MPCD cell size - /*! - * \param cell_size Grid spacing - * \note Calling forces a resize of the cell list on the next update - */ - void setCellSize(Scalar cell_size) - { - m_cell_size = cell_size; - m_max_grid_shift = 0.5 * m_cell_size; - m_needs_compute_dim = true; - } + //! Get the MPCD cell size (deprecated) + Scalar3 getCellSize(); - //! Get the MPCD cell size - Scalar getCellSize() const - { - return m_cell_size; - } + //! Set the MPCD cell size (deprecated) + void setCellSize(Scalar cell_size); //! Get the box that is covered by the cell list /*! @@ -189,29 +182,27 @@ class PYBIND11_EXPORT CellList : public Compute } } - //! Get the maximum permitted grid shift - const Scalar getMaxGridShift() const + //! Get the maximum permitted grid shift (fractional coordinates) + const Scalar3 getMaxGridShift() { + computeDimensions(); return m_max_grid_shift; } - // Get the grid shift vector + // Get the grid shift vector (fractional coordinates) const Scalar3& getGridShift() const { return m_grid_shift; } - //! Set the grid shift vector + //! Set the grid shift vector (fractional coordinates) void setGridShift(const Scalar3& shift) { - if (std::fabs(shift.x) > m_max_grid_shift || std::fabs(shift.y) > m_max_grid_shift - || std::fabs(shift.z) > m_max_grid_shift) + const Scalar3 max_grid_shift = getMaxGridShift(); + if (std::fabs(shift.x) > max_grid_shift.x || std::fabs(shift.y) > max_grid_shift.y + || std::fabs(shift.z) > max_grid_shift.z) { - m_exec_conf->msg->error() - << "mpcd: Specified cell list grid shift (" << shift.x << ", " << shift.y << ", " - << shift.z << ")" << std::endl - << "exceeds maximum component magnitude " << m_max_grid_shift << std::endl; - throw std::runtime_error("Error setting MPCD grid shift"); + throw std::runtime_error("MPCD grid shift out of range"); } m_grid_shift = shift; @@ -220,9 +211,6 @@ class PYBIND11_EXPORT CellList : public Compute //! Generates the random grid shift vector void drawGridShift(uint64_t timestep); - //! Calculate current cell occupancy statistics - virtual void getCellStatistics() const; - //! Gets the group of particles that is coupled to the MPCD solvent through the collision step std::shared_ptr getEmbeddedGroup() const { @@ -261,14 +249,14 @@ class PYBIND11_EXPORT CellList : public Compute bool m_enable_grid_shift; //!< Flag to enable grid shifting Scalar3 m_grid_shift; //!< Amount to shift particle positions when computing cell list - Scalar m_max_grid_shift; //!< Maximum amount grid can be shifted in any direction + Scalar3 m_max_grid_shift; //!< Maximum amount grid can be shifted in any direction //! Allocates internal data arrays virtual void reallocate(); - Scalar m_cell_size; //!< MPCD cell width uint3 m_cell_dim; //!< Number of cells in each direction uint3 m_global_cell_dim; //!< Number of cells in each direction of global simulation box + Scalar3 m_global_cell_dim_inv; //!< Inverse of number of cells in each direction of global box Index3D m_cell_indexer; //!< Indexer from 3D into cell list 1D Index3D m_global_cell_indexer; //!< Indexer from 3D into 1D for global cell indexes Index2D m_cell_list_indexer; //!< Indexer into cell list members @@ -337,9 +325,6 @@ class PYBIND11_EXPORT CellList : public Compute #ifdef ENABLE_MPI std::shared_ptr m_decomposition; - - //! Checks neighboring domains to make sure they are properly overlapping - void checkDomainBoundaries(); #endif // ENABLE_MPI }; } // end namespace mpcd diff --git a/hoomd/mpcd/CellListGPU.cc b/hoomd/mpcd/CellListGPU.cc index 3b0cee9a2f..f4d75ec72b 100644 --- a/hoomd/mpcd/CellListGPU.cc +++ b/hoomd/mpcd/CellListGPU.cc @@ -35,6 +35,30 @@ mpcd::CellListGPU::CellListGPU(std::shared_ptr sysdef, #endif // ENABLE_MPI } +mpcd::CellListGPU::CellListGPU(std::shared_ptr sysdef, + const uint3& global_cell_dim, + bool shift) + : mpcd::CellList(sysdef, global_cell_dim, shift) + { + m_tuner_cell.reset(new Autotuner<1>({AutotunerBase::makeBlockSizeRange(m_exec_conf)}, + m_exec_conf, + "mpcd_cell")); + m_tuner_sort.reset(new Autotuner<1>({AutotunerBase::makeBlockSizeRange(m_exec_conf)}, + m_exec_conf, + "mpcd_cell_sort")); + m_autotuners.insert(m_autotuners.end(), {m_tuner_cell, m_tuner_sort}); + +#ifdef ENABLE_MPI + m_tuner_embed_migrate.reset(new Autotuner<1>({AutotunerBase::makeBlockSizeRange(m_exec_conf)}, + m_exec_conf, + "mpcd_cell_embed_migrate")); + m_autotuners.push_back(m_tuner_embed_migrate); + + GPUFlags migrate_flag(m_exec_conf); + m_migrate_flag.swap(migrate_flag); +#endif // ENABLE_MPI + } + mpcd::CellListGPU::~CellListGPU() { } void mpcd::CellListGPU::buildCellList() @@ -90,9 +114,9 @@ void mpcd::CellListGPU::buildCellList() m_pdata->getBox().getPeriodic(), m_origin_idx, m_grid_shift, - m_pdata->getGlobalBox().getLo(), + m_pdata->getGlobalBox(), n_global_cells, - m_cell_size, + m_global_cell_dim, m_cell_np_max, m_cell_indexer, m_cell_list_indexer, @@ -117,9 +141,9 @@ void mpcd::CellListGPU::buildCellList() m_pdata->getBox().getPeriodic(), m_origin_idx, m_grid_shift, - m_pdata->getGlobalBox().getLo(), + m_pdata->getGlobalBox(), n_global_cells, - m_cell_size, + m_global_cell_dim, m_cell_np_max, m_cell_indexer, m_cell_list_indexer, diff --git a/hoomd/mpcd/CellListGPU.cu b/hoomd/mpcd/CellListGPU.cu index f1e511f79d..146b5f0483 100644 --- a/hoomd/mpcd/CellListGPU.cu +++ b/hoomd/mpcd/CellListGPU.cu @@ -29,9 +29,9 @@ namespace kernel * \param periodic Flags if local simulation is periodic * \param origin_idx Global origin index for the local box * \param grid_shift Random grid shift vector - * \param global_lo Lower bound of global orthorhombic simulation box + * \param global_box Global simulation box * \param n_global_cell Global dimensions of the cell list, including padding - * \param cell_size Cell width + * \param global_cell_dim Global cell dimensions, no padding * \param cell_np_max Maximum number of particles per cell * \param cell_indexer 3D indexer for cell id * \param cell_list_indexer 2D indexer for particle position in cell @@ -56,9 +56,9 @@ __global__ void compute_cell_list(unsigned int* d_cell_np, const uchar3 periodic, const int3 origin_idx, const Scalar3 grid_shift, - const Scalar3 global_lo, + const BoxDim global_box, const uint3 n_global_cell, - const Scalar cell_size, + const uint3 global_cell_dim, const unsigned int cell_np_max, const Index3D cell_indexer, const Index2D cell_list_indexer, @@ -87,11 +87,11 @@ __global__ void compute_cell_list(unsigned int* d_cell_np, return; } - // bin particle with grid shift assuming orthorhombic box (already validated) - const Scalar3 delta = (pos_i - grid_shift) - global_lo; - int3 global_bin = make_int3(std::floor(delta.x / cell_size), - std::floor(delta.y / cell_size), - std::floor(delta.z / cell_size)); + // bin particle with grid shift + const Scalar3 fractional_pos_i = global_box.makeFraction(pos_i) - grid_shift; + int3 global_bin = make_int3((int)std::floor(fractional_pos_i.x * global_cell_dim.x), + (int)std::floor(fractional_pos_i.y * global_cell_dim.y), + (int)std::floor(fractional_pos_i.z * global_cell_dim.z)); // wrap cell back through the boundaries (grid shifting may send +/- 1 outside of range) // this is done using periodic from the "local" box, since this will be periodic @@ -122,6 +122,28 @@ __global__ void compute_cell_list(unsigned int* d_cell_np, int3 bin = make_int3(global_bin.x - origin_idx.x, global_bin.y - origin_idx.y, global_bin.z - origin_idx.z); + // these checks guard against round-off errors with domain decomposition + if (!periodic.x) + { + if (bin.x == -1) + bin.x = 0; + else if (bin.x == (int)cell_indexer.getW()) + bin.x = cell_indexer.getW() - 1; + } + if (!periodic.y) + { + if (bin.y == -1) + bin.y = 0; + else if (bin.y == (int)cell_indexer.getH()) + bin.y = cell_indexer.getH() - 1; + } + if (!periodic.z) + { + if (bin.z == -1) + bin.z = 0; + else if (bin.z == (int)cell_indexer.getD()) + bin.z = cell_indexer.getD() - 1; + } // validate and make sure no particles blew out of the box if ((bin.x < 0 || bin.x >= (int)cell_indexer.getW()) @@ -185,13 +207,12 @@ __global__ void cell_check_migrate_embed(unsigned int* d_migrate_flag, const Scalar4 postype = d_pos[idx]; const Scalar3 pos = make_scalar3(postype.x, postype.y, postype.z); - const Scalar3 lo = box.getLo(); - const Scalar3 hi = box.getHi(); const uchar3 periodic = box.getPeriodic(); - - if ((!periodic.x && (pos.x >= hi.x || pos.x < lo.x)) - || (!periodic.y && (pos.y >= hi.y || pos.y < lo.y)) - || (!periodic.z && num_dim == 3 && (pos.z >= hi.z || pos.z < lo.z))) + const Scalar3 fractional_pos = box.makeFraction(pos); + if ((!periodic.x && (fractional_pos.x >= Scalar(1.0) || fractional_pos.x < Scalar(0.0))) + || (!periodic.y && (fractional_pos.y >= Scalar(1.0) || fractional_pos.y < Scalar(0.0))) + || (!periodic.z && num_dim == 3 + && (fractional_pos.z >= Scalar(1.0) || fractional_pos.z < Scalar(0.0)))) { atomicMax(d_migrate_flag, 1); } @@ -242,9 +263,9 @@ __global__ void cell_apply_sort(unsigned int* d_cell_list, * \param periodic Flags if local simulation is periodic * \param origin_idx Global origin index for the local box * \param grid_shift Random grid shift vector - * \param global_lo Lower bound of global orthorhombic simulation box + * \param global_box Global simulation box * \param n_global_cell Global dimensions of the cell list, including padding - * \param cell_size Cell width + * \param global_cell_dim Global cell dimensions, no padding * \param cell_np_max Maximum number of particles per cell * \param cell_indexer 3D indexer for cell id * \param cell_list_indexer 2D indexer for particle position in cell @@ -265,9 +286,9 @@ cudaError_t mpcd::gpu::compute_cell_list(unsigned int* d_cell_np, const uchar3& periodic, const int3& origin_idx, const Scalar3& grid_shift, - const Scalar3& global_lo, + const BoxDim& global_box, const uint3& n_global_cell, - const Scalar cell_size, + const uint3& global_cell_dim, const unsigned int cell_np_max, const Index3D& cell_indexer, const Index2D& cell_list_indexer, @@ -299,9 +320,9 @@ cudaError_t mpcd::gpu::compute_cell_list(unsigned int* d_cell_np, periodic, origin_idx, grid_shift, - global_lo, + global_box, n_global_cell, - cell_size, + global_cell_dim, cell_np_max, cell_indexer, cell_list_indexer, diff --git a/hoomd/mpcd/CellListGPU.cuh b/hoomd/mpcd/CellListGPU.cuh index dec9bf8a5c..3e84d9eefd 100644 --- a/hoomd/mpcd/CellListGPU.cuh +++ b/hoomd/mpcd/CellListGPU.cuh @@ -33,9 +33,9 @@ cudaError_t compute_cell_list(unsigned int* d_cell_np, const uchar3& periodic, const int3& origin_idx, const Scalar3& grid_shift, - const Scalar3& global_lo, + const BoxDim& global_box, const uint3& n_global_cell, - const Scalar cell_size, + const uint3& global_cell_dim, const unsigned int cell_np_max, const Index3D& cell_indexer, const Index2D& cell_list_indexer, diff --git a/hoomd/mpcd/CellListGPU.h b/hoomd/mpcd/CellListGPU.h index 24e3f00530..f468988778 100644 --- a/hoomd/mpcd/CellListGPU.h +++ b/hoomd/mpcd/CellListGPU.h @@ -24,9 +24,12 @@ namespace mpcd class PYBIND11_EXPORT CellListGPU : public mpcd::CellList { public: - //! Constructor + //! Constructor by size (deprecated) CellListGPU(std::shared_ptr sysdef, Scalar cell_size, bool shift); + //! Constructor by dimension + CellListGPU(std::shared_ptr sysdef, const uint3& global_cell_dim, bool shift); + virtual ~CellListGPU(); protected: diff --git a/hoomd/mpcd/Communicator.cc b/hoomd/mpcd/Communicator.cc index 1ccf25f28e..a83f7e852a 100644 --- a/hoomd/mpcd/Communicator.cc +++ b/hoomd/mpcd/Communicator.cc @@ -460,27 +460,26 @@ void mpcd::Communicator::setCommFlags(const BoxDim& box) access_mode::overwrite); // since box is orthorhombic, just use branching to compute comm flags - const Scalar3 lo = box.getLo(); - const Scalar3 hi = box.getHi(); for (unsigned int idx = 0; idx < N; ++idx) { const Scalar4& postype = h_pos.data[idx]; const Scalar3 pos = make_scalar3(postype.x, postype.y, postype.z); + const Scalar3 f = box.makeFraction(pos); unsigned int flags = 0; - if (pos.x >= hi.x) + if (f.x >= Scalar(1.0)) flags |= static_cast(mpcd::detail::send_mask::east); - else if (pos.x < lo.x) + else if (f.x < Scalar(0.0)) flags |= static_cast(mpcd::detail::send_mask::west); - if (pos.y >= hi.y) + if (f.y >= Scalar(1.0)) flags |= static_cast(mpcd::detail::send_mask::north); - else if (pos.y < lo.y) + else if (f.y < Scalar(0.0)) flags |= static_cast(mpcd::detail::send_mask::south); - if (pos.z >= hi.z) + if (f.z >= Scalar(1.0)) flags |= static_cast(mpcd::detail::send_mask::up); - else if (pos.z < lo.z) + else if (f.z < Scalar(0.0)) flags |= static_cast(mpcd::detail::send_mask::down); h_comm_flag.data[idx] = flags; @@ -654,7 +653,10 @@ BoxDim mpcd::Communicator::getWrapBox(const BoxDim& box) periodic.y = (isCommunicating(mpcd::detail::face::north)) ? 1 : 0; periodic.z = (isCommunicating(mpcd::detail::face::up)) ? 1 : 0; - return BoxDim(global_lo + shift, global_hi + shift, periodic); + BoxDim wrap_box(global_box); + wrap_box.setLoHi(global_lo + shift, global_hi + shift); + wrap_box.setPeriodic(periodic); + return wrap_box; } void mpcd::Communicator::attachCallbacks() diff --git a/hoomd/mpcd/CommunicatorGPU.cu b/hoomd/mpcd/CommunicatorGPU.cu index 1cdc338f0d..91c5ff195f 100644 --- a/hoomd/mpcd/CommunicatorGPU.cu +++ b/hoomd/mpcd/CommunicatorGPU.cu @@ -50,21 +50,22 @@ stage_particles(unsigned int* d_comm_flag, const Scalar4* d_pos, unsigned int N, const Scalar4 postype = d_pos[idx]; const Scalar3 pos = make_scalar3(postype.x, postype.y, postype.z); - const Scalar3 lo = box.getLo(); - const Scalar3 hi = box.getHi(); + const Scalar3 f = box.makeFraction(pos); unsigned int flags = 0; - if (pos.x >= hi.x) + if (f.x >= Scalar(1.0)) flags |= static_cast(mpcd::detail::send_mask::east); - else if (pos.x < lo.x) + else if (f.x < Scalar(0.0)) flags |= static_cast(mpcd::detail::send_mask::west); - if (pos.y >= hi.y) + + if (f.y >= Scalar(1.0)) flags |= static_cast(mpcd::detail::send_mask::north); - else if (pos.y < lo.y) + else if (f.y < Scalar(0.0)) flags |= static_cast(mpcd::detail::send_mask::south); - if (pos.z >= hi.z) + + if (f.z >= Scalar(1.0)) flags |= static_cast(mpcd::detail::send_mask::up); - else if (pos.z < lo.z) + else if (f.z < Scalar(0.0)) flags |= static_cast(mpcd::detail::send_mask::down); d_comm_flag[idx] = flags; diff --git a/hoomd/mpcd/ParallelPlateGeometryFiller.cc b/hoomd/mpcd/ParallelPlateGeometryFiller.cc index 149268f9e6..30101e9b55 100644 --- a/hoomd/mpcd/ParallelPlateGeometryFiller.cc +++ b/hoomd/mpcd/ParallelPlateGeometryFiller.cc @@ -28,10 +28,21 @@ mpcd::ParallelPlateGeometryFiller::~ParallelPlateGeometryFiller() m_exec_conf->msg->notice(5) << "Destroying MPCD ParallelPlateGeometryFiller" << std::endl; } +void mpcd::ParallelPlateGeometryFiller::fill(uint64_t timestep) + { + const BoxDim& box = m_pdata->getBox(); + if (box.getTiltFactorXY() != Scalar(0.0) || box.getTiltFactorXZ() != Scalar(0.0) + || box.getTiltFactorYZ() != Scalar(0.0)) + { + throw std::runtime_error("ParallelPlateGeometryFiller does not work with skewed boxes"); + } + mpcd::ManualVirtualParticleFiller::fill(timestep); + } + void mpcd::ParallelPlateGeometryFiller::computeNumFill() { const BoxDim& global_box = m_pdata->getGlobalBox(); - const Scalar cell_size = m_cl->getCellSize(); + const Scalar cell_size = m_cl->getCellSize().y; // box and slit geometry const BoxDim& box = m_pdata->getBox(); @@ -49,7 +60,7 @@ void mpcd::ParallelPlateGeometryFiller::computeNumFill() * This is done by round the walls onto the cell grid away from zero, and then including the * max shift of this cell edge. */ - const Scalar max_shift = m_cl->getMaxGridShift(); + const Scalar max_shift = m_cl->getMaxGridShift().y * global_box.getL().y; const Scalar global_lo = global_box.getLo().y; if (box.getHi().y >= H) { diff --git a/hoomd/mpcd/ParallelPlateGeometryFiller.h b/hoomd/mpcd/ParallelPlateGeometryFiller.h index c4d45ccabd..0389bd0119 100644 --- a/hoomd/mpcd/ParallelPlateGeometryFiller.h +++ b/hoomd/mpcd/ParallelPlateGeometryFiller.h @@ -38,6 +38,8 @@ class PYBIND11_EXPORT ParallelPlateGeometryFiller : public mpcd::ManualVirtualPa virtual ~ParallelPlateGeometryFiller(); + virtual void fill(uint64_t timestep) override; + std::shared_ptr getGeometry() const { return m_geom; diff --git a/hoomd/mpcd/PlanarPoreGeometryFiller.cc b/hoomd/mpcd/PlanarPoreGeometryFiller.cc index 31d9210df5..7a836e1b5e 100644 --- a/hoomd/mpcd/PlanarPoreGeometryFiller.cc +++ b/hoomd/mpcd/PlanarPoreGeometryFiller.cc @@ -29,7 +29,7 @@ mpcd::PlanarPoreGeometryFiller::PlanarPoreGeometryFiller( // unphysical values in cache to always force recompute m_needs_recompute = true; - m_recompute_cache = make_scalar3(-1, -1, -1); + m_recompute_cache = make_scalar4(-1, -1, -1, -1); m_pdata->getBoxChangeSignal() .connect( this); @@ -43,23 +43,39 @@ mpcd::PlanarPoreGeometryFiller::~PlanarPoreGeometryFiller() &mpcd::PlanarPoreGeometryFiller::notifyRecompute>(this); } +void mpcd::PlanarPoreGeometryFiller::fill(uint64_t timestep) + { + const BoxDim& box = m_pdata->getBox(); + if (box.getTiltFactorXY() != Scalar(0.0) || box.getTiltFactorXZ() != Scalar(0.0) + || box.getTiltFactorYZ() != Scalar(0.0)) + { + throw std::runtime_error("PlanarPoreGeometryFiller does not work with skewed boxes"); + } + mpcd::ManualVirtualParticleFiller::fill(timestep); + } + void mpcd::PlanarPoreGeometryFiller::computeNumFill() { - const Scalar cell_size = m_cl->getCellSize(); - const Scalar max_shift = m_cl->getMaxGridShift(); + const Scalar3 cell_size_vector = m_cl->getCellSize(); + if (fabs(cell_size_vector.x - cell_size_vector.y) > Scalar(1e-6) + || fabs(cell_size_vector.x - cell_size_vector.z) > Scalar(1e-6)) + { + throw std::runtime_error("Cell size must be constant"); + } + const Scalar cell_size = cell_size_vector.y; + const BoxDim& global_box = m_pdata->getGlobalBox(); + const Scalar3 max_shift = m_cl->getMaxGridShift() * global_box.getL(); // check if fill-relevant variables have changed (can't use signal because cell list build may // not have triggered yet) - m_needs_recompute |= (m_recompute_cache.x != cell_size || m_recompute_cache.y != max_shift - || m_recompute_cache.z != m_density); + m_needs_recompute + |= (m_recompute_cache.x != cell_size || m_recompute_cache.y != max_shift.x + || m_recompute_cache.z != max_shift.y || m_recompute_cache.w != m_density); // only recompute if needed if (!m_needs_recompute) return; - // as a precaution, validate the global box with the current cell list - const BoxDim& global_box = m_pdata->getGlobalBox(); - // box and slit geometry const BoxDim& box = m_pdata->getBox(); const Scalar3 lo = box.getLo(); @@ -77,13 +93,13 @@ void mpcd::PlanarPoreGeometryFiller::computeNumFill() const Scalar3 global_hi = global_box.getHi(); Scalar2 x_bounds, y_bounds; // upper bound on lower wall in x - x_bounds.x = cell_size * std::ceil((-L - global_lo.x) / cell_size) + global_lo.x + max_shift; + x_bounds.x = cell_size * std::ceil((-L - global_lo.x) / cell_size) + global_lo.x + max_shift.x; // lower bound on upper wall in x - x_bounds.y = cell_size * std::floor((L - global_lo.x) / cell_size) + global_lo.x - max_shift; + x_bounds.y = cell_size * std::floor((L - global_lo.x) / cell_size) + global_lo.x - max_shift.x; // lower bound on lower wall in y - y_bounds.x = cell_size * std::floor((-H - global_lo.y) / cell_size) + global_lo.y - max_shift; + y_bounds.x = cell_size * std::floor((-H - global_lo.y) / cell_size) + global_lo.y - max_shift.y; // upper bound on upper wall in y - y_bounds.y = cell_size * std::ceil((H - global_lo.y) / cell_size) + global_lo.y + max_shift; + y_bounds.y = cell_size * std::ceil((H - global_lo.y) / cell_size) + global_lo.y + max_shift.y; // define the 6 2D bounding boxes (lo.x,hi.x,lo.y,hi.y) for filling in this geometry (z is // infinite) (this is essentially a U shape inside the pore). @@ -130,7 +146,7 @@ void mpcd::PlanarPoreGeometryFiller::computeNumFill() // size is now updated, cache the cell dimensions used m_needs_recompute = false; - m_recompute_cache = make_scalar3(cell_size, max_shift, m_density); + m_recompute_cache = make_scalar4(cell_size, max_shift.x, max_shift.y, m_density); } /*! diff --git a/hoomd/mpcd/PlanarPoreGeometryFiller.h b/hoomd/mpcd/PlanarPoreGeometryFiller.h index 36ef35a1e9..fa6b96f6d1 100644 --- a/hoomd/mpcd/PlanarPoreGeometryFiller.h +++ b/hoomd/mpcd/PlanarPoreGeometryFiller.h @@ -38,6 +38,8 @@ class PYBIND11_EXPORT PlanarPoreGeometryFiller : public mpcd::ManualVirtualParti virtual ~PlanarPoreGeometryFiller(); + virtual void fill(uint64_t timestep) override; + std::shared_ptr getGeometry() const { return m_geom; @@ -65,7 +67,7 @@ class PYBIND11_EXPORT PlanarPoreGeometryFiller : public mpcd::ManualVirtualParti private: bool m_needs_recompute; - Scalar3 m_recompute_cache; + Scalar4 m_recompute_cache; void notifyRecompute() { m_needs_recompute = true; diff --git a/hoomd/mpcd/RejectionVirtualParticleFiller.h b/hoomd/mpcd/RejectionVirtualParticleFiller.h index 3c9b15b070..fdedb2bf7f 100644 --- a/hoomd/mpcd/RejectionVirtualParticleFiller.h +++ b/hoomd/mpcd/RejectionVirtualParticleFiller.h @@ -80,8 +80,14 @@ class PYBIND11_EXPORT RejectionVirtualParticleFiller : public mpcd::VirtualParti template void RejectionVirtualParticleFiller::fill(uint64_t timestep) { - // Number of particles that we need to draw (constant) const BoxDim& box = m_pdata->getBox(); + if (box.getTiltFactorXY() != Scalar(0.0) || box.getTiltFactorXZ() != Scalar(0.0) + || box.getTiltFactorYZ() != Scalar(0.0)) + { + throw std::runtime_error("Rejection particle filler does not work with skewed boxes"); + } + + // Number of particles that we need to draw (constant) const Scalar3 lo = box.getLo(); const Scalar3 hi = box.getHi(); const unsigned int num_virtual_max diff --git a/hoomd/mpcd/RejectionVirtualParticleFillerGPU.h b/hoomd/mpcd/RejectionVirtualParticleFillerGPU.h index e28f3afb67..0fc84c1bdb 100644 --- a/hoomd/mpcd/RejectionVirtualParticleFillerGPU.h +++ b/hoomd/mpcd/RejectionVirtualParticleFillerGPU.h @@ -66,8 +66,14 @@ class PYBIND11_EXPORT RejectionVirtualParticleFillerGPU template void RejectionVirtualParticleFillerGPU::fill(uint64_t timestep) { - // Number of particles that we need to draw (constant) const BoxDim& box = this->m_pdata->getBox(); + if (box.getTiltFactorXY() != Scalar(0.0) || box.getTiltFactorXZ() != Scalar(0.0) + || box.getTiltFactorYZ() != Scalar(0.0)) + { + throw std::runtime_error("Rejection particle filler does not work with skewed boxes"); + } + + // Number of particles that we need to draw (constant) const Scalar3 lo = box.getLo(); const Scalar3 hi = box.getHi(); const unsigned int num_virtual_max diff --git a/hoomd/mpcd/collide.py b/hoomd/mpcd/collide.py index 94a1a72f4c..1f8d96ba96 100644 --- a/hoomd/mpcd/collide.py +++ b/hoomd/mpcd/collide.py @@ -29,8 +29,10 @@ class CellList(Compute): Args: shift (bool): When True, randomly shift underlying collision cells. - The MPCD `CellList` bins particles into cubic cells of edge length 1.0. - The simulation box must be orthorhombic, and its edges must be an integer. + The MPCD `CellList` bins particles into cells aligned with the lattice + vectors that define the simulation box. The default number of cells along + each lattice vector is computed from :math:`L_x`, :math:`L_y`, and + :math:`L_z` with a length of 1.0. When the total mean-free path of the MPCD particles is small, the cells should be randomly shifted in order to ensure Galilean invariance of the @@ -85,6 +87,11 @@ def _attach_hook(self): super()._attach_hook() + @property + def num_cells(self): + """tuple[int]: Number of cells along each lattice vector.""" + return self._cpp_obj.num_cells + class CollisionMethod(Operation): """Base collision method. diff --git a/hoomd/mpcd/fill.py b/hoomd/mpcd/fill.py index 4b6b2438d0..b3b5e97929 100644 --- a/hoomd/mpcd/fill.py +++ b/hoomd/mpcd/fill.py @@ -131,6 +131,13 @@ class GeometryFiller(VirtualParticleFiller): specified `geometry`. The algorithm for doing the filling depends on the specific `geometry`. + .. rubric:: Limitations: + + This filler **does not** currently support triclinic boxes for any + :class:`~hoomd.mpcd.geometry.Geometry`. Additionally, this filler does not + support the :class:`~hoomd.mpcd.geometry.PlanarPore` geometry for any + non-cubic cell shape. Exceptions will be raised in these cases. + .. rubric:: Example: Filler for parallel plate geometry. diff --git a/hoomd/mpcd/pytest/test_collide.py b/hoomd/mpcd/pytest/test_collide.py index 0db7c21266..04d3a1dddc 100644 --- a/hoomd/mpcd/pytest/test_collide.py +++ b/hoomd/mpcd/pytest/test_collide.py @@ -19,6 +19,17 @@ def small_snap(): return snap +def test_cell_list(small_snap, simulation_factory): + if small_snap.communicator.rank == 0: + small_snap.configuration.box = [20, 30, 40, 0, 0, 0] + sim = simulation_factory(small_snap) + + cl = hoomd.mpcd.collide.CellList() + + cl._attach(sim) + assert cl.num_cells == (20, 30, 40) + + @pytest.mark.parametrize( "cls, init_args", [ diff --git a/hoomd/mpcd/test/cell_communicator_mpi_test.cc b/hoomd/mpcd/test/cell_communicator_mpi_test.cc index f7e105ad4a..130afd1bb2 100644 --- a/hoomd/mpcd/test/cell_communicator_mpi_test.cc +++ b/hoomd/mpcd/test/cell_communicator_mpi_test.cc @@ -155,7 +155,7 @@ void cell_communicator_overdecompose_test(std::shared_ptr pdata_comm(new Communicator(sysdef, decomposition)); sysdef->setCommunicator(pdata_comm); - auto cl = std::make_shared(sysdef, 1.0, false); + auto cl = std::make_shared(sysdef, make_uint3(6, 6, 6), false); cl->computeDimensions(); // Don't really care what's in this array, just want to make sure errors get thrown @@ -191,20 +191,20 @@ void cell_communicator_overdecompose_test(std::shared_ptrsetCellSize(0.5); + cl->setGlobalDim(make_uint3(12, 12, 12)); cl->compute(3); props.resize(cl->getNCells()); comm.communicate(props, pack_op); // shrink the box size to the minimum that can be decomposed cl->setNExtraCells(0); - cl->setCellSize(2.0); + cl->setGlobalDim(make_uint3(3, 3, 3)); cl->compute(4); props.resize(cl->getNCells()); comm.communicate(props, pack_op); // now shrink further to ensure failure - cl->setCellSize(3.0); + cl->setGlobalDim(make_uint3(2, 2, 2)); cl->compute(5); props.resize(cl->getNCells()); UP_ASSERT_EXCEPTION(std::runtime_error, [&] { comm.communicate(props, pack_op); }); diff --git a/hoomd/mpcd/test/cell_list_mpi_test.cc b/hoomd/mpcd/test/cell_list_mpi_test.cc index 3af0996f66..43205a03e9 100644 --- a/hoomd/mpcd/test/cell_list_mpi_test.cc +++ b/hoomd/mpcd/test/cell_list_mpi_test.cc @@ -11,10 +11,145 @@ #include "hoomd/mpcd/Communicator.h" #include "hoomd/test/upp11_config.h" +#include "utils.h" + HOOMD_UP_MAIN() using namespace hoomd; +void checkDomainBoundaries(std::shared_ptr sysdef, + std::shared_ptr cl) + { + auto pdata = sysdef->getParticleData(); + auto exec_conf = pdata->getExecConf(); + MPI_Comm mpi_comm = exec_conf->getMPICommunicator(); + auto decomposition = pdata->getDomainDecomposition(); + + auto num_comm = cl->getNComm(); + auto origin_idx = cl->getOriginIndex(); + auto cell_dim = cl->getDim(); + auto num_extra = cl->getNExtraCells(); + + for (unsigned int dir = 0; dir < num_comm.size(); ++dir) + { + mpcd::detail::face d = static_cast(dir); + if (!cl->isCommunicating(d)) + continue; + + // receive in the opposite direction from which we send + unsigned int send_neighbor = decomposition->getNeighborRank(dir); + unsigned int recv_neighbor; + if (dir % 2 == 0) + recv_neighbor = decomposition->getNeighborRank(dir + 1); + else + recv_neighbor = decomposition->getNeighborRank(dir - 1); + + // first make sure each dimension is sending and receiving the same size data + MPI_Request reqs[2]; + MPI_Status status[2]; + + // check that the number received is the same as that being sent from neighbor + unsigned int n_send = num_comm[dir]; + unsigned int n_expect_recv; + if (dir % 2 == 0) + n_expect_recv = num_comm[dir + 1]; + else + n_expect_recv = num_comm[dir - 1]; + + unsigned int n_recv; + MPI_Isend(&n_send, 1, MPI_UNSIGNED, send_neighbor, 0, mpi_comm, &reqs[0]); + MPI_Irecv(&n_recv, 1, MPI_UNSIGNED, recv_neighbor, 0, mpi_comm, &reqs[1]); + MPI_Waitall(2, reqs, status); + UP_ASSERT_EQUAL(n_recv, n_expect_recv); + + // check that the same cell ids are communicated + std::vector send_cells(n_send), recv_cells(n_recv); + for (unsigned int i = 0; i < n_send; ++i) + { + if (d == mpcd::detail::face::east) + { + send_cells[i] = origin_idx.x + cell_dim.x - num_extra - n_send + i; + } + else if (d == mpcd::detail::face::west) + { + send_cells[i] = origin_idx.x + i; + } + else if (d == mpcd::detail::face::north) + { + send_cells[i] = origin_idx.y + cell_dim.y - num_extra - n_send + i; + } + else if (d == mpcd::detail::face::south) + { + send_cells[i] = origin_idx.y + i; + } + else if (d == mpcd::detail::face::up) + { + send_cells[i] = origin_idx.z + cell_dim.z - num_extra - n_send + i; + } + else if (d == mpcd::detail::face::down) + { + send_cells[i] = origin_idx.z + i; + } + } + + MPI_Isend(&send_cells[0], n_send, MPI_INT, send_neighbor, 1, mpi_comm, &reqs[0]); + MPI_Irecv(&recv_cells[0], n_recv, MPI_INT, recv_neighbor, 1, mpi_comm, &reqs[1]); + MPI_Waitall(2, reqs, status); + + for (unsigned int i = 0; i < n_recv; ++i) + { + // wrap the received cell back into the global box + // only two of the entries will be valid, the others are dummies + int3 recv_cell = make_int3(0, 0, 0); + if (d == mpcd::detail::face::east || d == mpcd::detail::face::west) + { + recv_cell.x = recv_cells[i]; + } + else if (d == mpcd::detail::face::north || d == mpcd::detail::face::south) + { + recv_cell.y = recv_cells[i]; + } + else if (d == mpcd::detail::face::up || d == mpcd::detail::face::down) + { + recv_cell.z = recv_cells[i]; + } + recv_cell = cl->wrapGlobalCell(recv_cell); + + // compute the expected cell to receive, also wrapped + int3 expect_recv_cell = make_int3(0, 0, 0); + if (d == mpcd::detail::face::east) + { + expect_recv_cell.x = origin_idx.x + i; + } + else if (d == mpcd::detail::face::west) + { + expect_recv_cell.x = origin_idx.x + cell_dim.x - num_extra - n_recv + i; + } + else if (d == mpcd::detail::face::north) + { + expect_recv_cell.y = origin_idx.y + i; + } + else if (d == mpcd::detail::face::south) + { + expect_recv_cell.y = origin_idx.y + cell_dim.y - num_extra - n_recv + i; + } + else if (d == mpcd::detail::face::up) + { + expect_recv_cell.z = origin_idx.z + i; + } + else if (d == mpcd::detail::face::down) + { + expect_recv_cell.z = origin_idx.z + cell_dim.z - num_extra - n_recv + i; + } + expect_recv_cell = cl->wrapGlobalCell(expect_recv_cell); + + UP_ASSERT_EQUAL(recv_cell.x, expect_recv_cell.x); + UP_ASSERT_EQUAL(recv_cell.y, expect_recv_cell.y); + UP_ASSERT_EQUAL(recv_cell.z, expect_recv_cell.z); + } + } + } + //! Test for correct calculation of MPCD grid dimensions /*! * \param exec_conf Execution configuration @@ -28,7 +163,8 @@ template void celllist_dimension_test(std::shared_ptr exec_conf, bool mpi_x, bool mpi_y, - bool mpi_z) + bool mpi_z, + const Scalar3& tilt) { // only run tests on first partition if (exec_conf->getPartition() != 0) @@ -36,6 +172,7 @@ void celllist_dimension_test(std::shared_ptr exec_conf, std::shared_ptr> snap(new SnapshotSystemData()); snap->global_box = std::make_shared(5.0); + snap->global_box->setTiltFactors(tilt.x, tilt.y, tilt.z); snap->particle_data.type_mapping.push_back("A"); snap->mpcd_data.resize(1); snap->mpcd_data.type_mapping.push_back("A"); @@ -74,11 +211,14 @@ void celllist_dimension_test(std::shared_ptr exec_conf, // initialize mpcd system auto pdata_1 = sysdef->getMPCDParticleData(); - std::shared_ptr cl(new CL(sysdef, 1.0, false)); + std::shared_ptr cl(new CL(sysdef, make_uint3(5, 5, 5), false)); // compute the cell list cl->computeDimensions(); + checkDomainBoundaries(sysdef, cl); + const bool is_orthorhombic = (tilt == make_scalar3(0, 0, 0)); + if (is_orthorhombic) { // check domain origins const int3 origin = cl->getOriginIndex(); @@ -139,7 +279,14 @@ void celllist_dimension_test(std::shared_ptr exec_conf, if (mpi_x) { // split evenly in x -> both domains are same size - UP_ASSERT_EQUAL(dim.x, 4); + if (pos.x) + { + UP_ASSERT_EQUAL(dim.x, 4); + } + else + { + UP_ASSERT_EQUAL(dim.x, 4); + } } else { @@ -181,52 +328,18 @@ void celllist_dimension_test(std::shared_ptr exec_conf, } std::array num_comm = cl->getNComm(); - if (mpi_x) - { - if (pos.x) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], 2); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], 1); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], 1); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], 2); - } - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], 0); - } - - if (mpi_y) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], 2); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], 2); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], 0); - } - - if (mpi_z) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], 2); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], 2); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], 0); - } - - // check for grid shifting errors - UP_ASSERT_EXCEPTION(std::runtime_error, - [&] { cl->setGridShift(make_scalar3(-0.51, -0.51, -0.51)); }); - UP_ASSERT_EXCEPTION(std::runtime_error, - [&] { cl->setGridShift(make_scalar3(0.51, 0.51, 0.51)); }); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], + (mpi_x) ? ((pos.x) ? 2 : 1) : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], + (mpi_x) ? ((pos.x) ? 1 : 2) : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], + (mpi_y) ? 2 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], + (mpi_y) ? 2 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], + (mpi_z) ? 2 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], + (mpi_z) ? 2 : 0); // check coverage box const BoxDim coverage = cl->getCoverageBox(); @@ -234,64 +347,66 @@ void celllist_dimension_test(std::shared_ptr exec_conf, { if (pos.x) { - CHECK_CLOSE(coverage.getLo().x, 0.0, tol); - CHECK_CLOSE(coverage.getHi().x, 3.0, tol); + UP_ASSERT_SMALL(coverage.getLo().x, tol); + UP_ASSERT_CLOSE(coverage.getHi().x, 3.0, tol); } else { - CHECK_CLOSE(coverage.getLo().x, -3.0, tol); - CHECK_CLOSE(coverage.getHi().x, 0.0, tol); + UP_ASSERT_CLOSE(coverage.getLo().x, -3.0, tol); + UP_ASSERT_SMALL(coverage.getHi().x, tol); } } else { - CHECK_CLOSE(coverage.getLo().x, -2.5, tol); - CHECK_CLOSE(coverage.getHi().x, 2.5, tol); + UP_ASSERT_CLOSE(coverage.getLo().x, -2.5, tol); + UP_ASSERT_CLOSE(coverage.getHi().x, 2.5, tol); } if (mpi_y) { if (pos.y) { - CHECK_CLOSE(coverage.getLo().y, -1.0, tol); - CHECK_CLOSE(coverage.getHi().y, 3.0, tol); + UP_ASSERT_CLOSE(coverage.getLo().y, -1.0, tol); + UP_ASSERT_CLOSE(coverage.getHi().y, 3.0, tol); } else { - CHECK_CLOSE(coverage.getLo().y, -3.0, tol); - CHECK_CLOSE(coverage.getHi().y, 0.0, tol); + UP_ASSERT_CLOSE(coverage.getLo().y, -3.0, tol); + UP_ASSERT_SMALL(coverage.getHi().y, tol); } } else { - CHECK_CLOSE(coverage.getLo().y, -2.5, tol); - CHECK_CLOSE(coverage.getHi().y, 2.5, tol); + UP_ASSERT_CLOSE(coverage.getLo().y, -2.5, tol); + UP_ASSERT_CLOSE(coverage.getHi().y, 2.5, tol); } if (mpi_z) { if (pos.z) { - CHECK_CLOSE(coverage.getLo().z, 0.0, tol); - CHECK_CLOSE(coverage.getHi().z, 3.0, tol); + UP_ASSERT_SMALL(coverage.getLo().z, tol); + UP_ASSERT_CLOSE(coverage.getHi().z, 3.0, tol); } else { - CHECK_CLOSE(coverage.getLo().z, -3.0, tol); - CHECK_CLOSE(coverage.getHi().z, 1.0, tol); + UP_ASSERT_CLOSE(coverage.getLo().z, -3.0, tol); + UP_ASSERT_CLOSE(coverage.getHi().z, 1.0, tol); } } else { - CHECK_CLOSE(coverage.getLo().z, -2.5, tol); - CHECK_CLOSE(coverage.getHi().z, 2.5, tol); + UP_ASSERT_CLOSE(coverage.getLo().z, -2.5, tol); + UP_ASSERT_CLOSE(coverage.getHi().z, 2.5, tol); } } /*******************/ // Change the cell size, and ensure everything stays up to date - cl->setCellSize(0.5); + cl->setGlobalDim(make_uint3(10, 10, 10)); cl->computeDimensions(); + checkDomainBoundaries(sysdef, cl); + if (is_orthorhombic) { // check domain origins const int3 origin = cl->getOriginIndex(); @@ -385,7 +500,9 @@ void celllist_dimension_test(std::shared_ptr exec_conf, } else { - UP_ASSERT_EQUAL(dim.z, 7); + // floating point rounding makes this 8 not 7 (extra cell communicated on this + // edge) + UP_ASSERT_EQUAL(dim.z, 8); } } else @@ -394,124 +511,86 @@ void celllist_dimension_test(std::shared_ptr exec_conf, } std::array num_comm = cl->getNComm(); - if (mpi_x) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], 2); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], 2); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], 0); - } - - if (mpi_y) - { - if (pos.y) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], 2); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], 1); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], 1); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], 2); - } - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], 0); - } - - if (mpi_z) - { - if (pos.z) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], 2); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], 1); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], 1); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], 2); - } - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], 0); - } - - UP_ASSERT_EXCEPTION(std::runtime_error, - [&] { cl->setGridShift(make_scalar3(-0.3, -0.3, -0.3)); }); - UP_ASSERT_EXCEPTION(std::runtime_error, - [&] { cl->setGridShift(make_scalar3(0.3, 0.3, 0.3)); }); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], + (mpi_x) ? 2 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], + (mpi_x) ? 2 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], + (mpi_y) ? ((pos.y) ? 2 : 1) : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], + (mpi_y) ? ((pos.y) ? 1 : 2) : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], + (mpi_z) ? 2 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], + (mpi_z) ? 2 : 0); const BoxDim coverage = cl->getCoverageBox(); if (mpi_x) { if (pos.x) { - CHECK_CLOSE(coverage.getLo().x, -0.25, tol); - CHECK_CLOSE(coverage.getHi().x, 2.75, tol); + UP_ASSERT_CLOSE(coverage.getLo().x, -0.25, tol); + UP_ASSERT_CLOSE(coverage.getHi().x, 2.75, tol); } else { - CHECK_CLOSE(coverage.getLo().x, -2.75, tol); - CHECK_CLOSE(coverage.getHi().x, 0.25, tol); + UP_ASSERT_CLOSE(coverage.getLo().x, -2.75, tol); + UP_ASSERT_CLOSE(coverage.getHi().x, 0.25, tol); } } else { - CHECK_CLOSE(coverage.getLo().x, -2.5, tol); - CHECK_CLOSE(coverage.getHi().x, 2.5, tol); + UP_ASSERT_CLOSE(coverage.getLo().x, -2.5, tol); + UP_ASSERT_CLOSE(coverage.getHi().x, 2.5, tol); } if (mpi_y) { if (pos.y) { - CHECK_CLOSE(coverage.getLo().y, -0.25, tol); - CHECK_CLOSE(coverage.getHi().y, 2.75, tol); + UP_ASSERT_CLOSE(coverage.getLo().y, -0.25, tol); + UP_ASSERT_CLOSE(coverage.getHi().y, 2.75, tol); } else { - CHECK_CLOSE(coverage.getLo().y, -2.75, tol); - CHECK_CLOSE(coverage.getHi().y, -0.25, tol); + UP_ASSERT_CLOSE(coverage.getLo().y, -2.75, tol); + UP_ASSERT_CLOSE(coverage.getHi().y, -0.25, tol); } } else { - CHECK_CLOSE(coverage.getLo().y, -2.5, tol); - CHECK_CLOSE(coverage.getHi().y, 2.5, tol); + UP_ASSERT_CLOSE(coverage.getLo().y, -2.5, tol); + UP_ASSERT_CLOSE(coverage.getHi().y, 2.5, tol); } if (mpi_z) { if (pos.z) { - CHECK_CLOSE(coverage.getLo().z, 0.25, tol); - CHECK_CLOSE(coverage.getHi().z, 2.75, tol); + UP_ASSERT_CLOSE(coverage.getLo().z, 0.25, tol); + UP_ASSERT_CLOSE(coverage.getHi().z, 2.75, tol); } else { - CHECK_CLOSE(coverage.getLo().z, -2.75, tol); - CHECK_CLOSE(coverage.getHi().z, 0.25, tol); + UP_ASSERT_CLOSE(coverage.getLo().z, -2.75, tol); + // floating point rounding makes this 0.75 not 0.25 + UP_ASSERT_CLOSE(coverage.getHi().z, 0.75, tol); } } else { - CHECK_CLOSE(coverage.getLo().z, -2.5, tol); - CHECK_CLOSE(coverage.getHi().z, 2.5, tol); + UP_ASSERT_CLOSE(coverage.getLo().z, -2.5, tol); + UP_ASSERT_CLOSE(coverage.getHi().z, 2.5, tol); } } /*******************/ - // Increase the number of communication cells. This will trigger an increase in the size of the - // diffusion layer + // Increase the number of communication cells. This will trigger an increase in the size of + // the diffusion layer cl->setNExtraCells(1); cl->computeDimensions(); + checkDomainBoundaries(sysdef, cl); + if (is_orthorhombic) { // all origins should be shifted down by 1 cell const int3 origin = cl->getOriginIndex(); @@ -599,7 +678,8 @@ void celllist_dimension_test(std::shared_ptr exec_conf, } else { - UP_ASSERT_EQUAL(dim.z, 9); + // floating point rounding makes thes 10 not 9 + UP_ASSERT_EQUAL(dim.z, 10); } } else @@ -609,59 +689,18 @@ void celllist_dimension_test(std::shared_ptr exec_conf, // all comms should be increased by 1 std::array num_comm = cl->getNComm(); - if (mpi_x) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], 3); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], 3); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], 0); - } - - if (mpi_y) - { - if (pos.y) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], 3); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], 2); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], 2); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], 3); - } - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], 0); - } - - if (mpi_z) - { - if (pos.z) - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], 3); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], 2); - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], 2); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], 3); - } - } - else - { - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], 0); - UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], 0); - } - - UP_ASSERT_EXCEPTION(std::runtime_error, - [&] { cl->setGridShift(make_scalar3(-0.3, -0.3, -0.3)); }); - UP_ASSERT_EXCEPTION(std::runtime_error, - [&] { cl->setGridShift(make_scalar3(0.3, 0.3, 0.3)); }); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::east)], + (mpi_x) ? 3 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::west)], + (mpi_x) ? 3 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::north)], + (mpi_y) ? ((pos.y) ? 3 : 2) : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::south)], + (mpi_y) ? ((pos.y) ? 2 : 3) : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::up)], + (mpi_z) ? 3 : 0); + UP_ASSERT_EQUAL(num_comm[static_cast(mpcd::detail::face::down)], + (mpi_z) ? 3 : 0); const BoxDim coverage = cl->getCoverageBox(); if (mpi_x) @@ -712,7 +751,8 @@ void celllist_dimension_test(std::shared_ptr exec_conf, else { CHECK_CLOSE(coverage.getLo().z, -3.25, tol); - CHECK_CLOSE(coverage.getHi().z, 0.75, tol); + // floating point rounding makes this 1.25 not 0.75 + CHECK_CLOSE(coverage.getHi().z, 1.25, tol); } } else @@ -724,12 +764,19 @@ void celllist_dimension_test(std::shared_ptr exec_conf, } //! Test for correct cell listing of a basic system -template void celllist_basic_test(std::shared_ptr exec_conf) +template +void celllist_basic_test(std::shared_ptr exec_conf, + const Scalar3& L, + const Scalar3& tilt) { UP_ASSERT_EQUAL(exec_conf->getNRanks(), 8); + auto ref_box = std::make_shared(6.0); + auto box = std::make_shared(L); + box->setTiltFactors(tilt.x, tilt.y, tilt.z); + std::shared_ptr> snap(new SnapshotSystemData()); - snap->global_box = std::make_shared(6.0); + snap->global_box = box; snap->particle_data.type_mapping.push_back("A"); // place each particle in the same cell, but on different ranks /* @@ -746,14 +793,14 @@ template void celllist_basic_test(std::shared_ptrmpcd_data.resize(8); snap->mpcd_data.type_mapping.push_back("A"); - snap->mpcd_data.position[0] = vec3(-0.1, -0.1, -0.1); - snap->mpcd_data.position[1] = vec3(0.1, -0.1, -0.1); - snap->mpcd_data.position[2] = vec3(-0.1, 0.1, -0.1); - snap->mpcd_data.position[3] = vec3(0.1, 0.1, -0.1); - snap->mpcd_data.position[4] = vec3(-0.1, -0.1, 0.1); - snap->mpcd_data.position[5] = vec3(0.1, -0.1, 0.1); - snap->mpcd_data.position[6] = vec3(-0.1, 0.1, 0.1); - snap->mpcd_data.position[7] = vec3(0.1, 0.1, 0.1); + snap->mpcd_data.position[0] = scale(vec3(-0.1, -0.1, -0.1), ref_box, box); + snap->mpcd_data.position[1] = scale(vec3(0.1, -0.1, -0.1), ref_box, box); + snap->mpcd_data.position[2] = scale(vec3(-0.1, 0.1, -0.1), ref_box, box); + snap->mpcd_data.position[3] = scale(vec3(0.1, 0.1, -0.1), ref_box, box); + snap->mpcd_data.position[4] = scale(vec3(-0.1, -0.1, 0.1), ref_box, box); + snap->mpcd_data.position[5] = scale(vec3(0.1, -0.1, 0.1), ref_box, box); + snap->mpcd_data.position[6] = scale(vec3(-0.1, 0.1, 0.1), ref_box, box); + snap->mpcd_data.position[7] = scale(vec3(0.1, 0.1, 0.1), ref_box, box); std::shared_ptr decomposition( new DomainDecomposition(exec_conf, snap->global_box->getL(), 2, 2, 2)); @@ -763,7 +810,7 @@ template void celllist_basic_test(std::shared_ptr pdata = sysdef->getMPCDParticleData(); - std::shared_ptr cl(new CL(sysdef, 1.0, false)); + std::shared_ptr cl(new CL(sysdef, make_uint3(6, 6, 6), false)); cl->compute(0); const unsigned int my_rank = exec_conf->getRank(); { @@ -824,7 +871,8 @@ template void celllist_basic_test(std::shared_ptrsetGridShift(make_scalar3(-0.5, -0.5, -0.5)); + const Scalar3 shift = (Scalar(0.5) / 6) * make_scalar3(1, 1, 1); + cl->setGridShift(-shift); cl->compute(1); { ArrayHandle h_cell_np(cl->getCellSizeArray(), @@ -884,7 +932,7 @@ template void celllist_basic_test(std::shared_ptrsetGridShift(make_scalar3(0.5, 0.5, 0.5)); + cl->setGridShift(shift); cl->compute(2); { ArrayHandle h_cell_np(cl->getCellSizeArray(), @@ -945,12 +993,20 @@ template void celllist_basic_test(std::shared_ptr void celllist_edge_test(std::shared_ptr exec_conf) +template +void celllist_edge_test(std::shared_ptr exec_conf, + const Scalar3& L, + const Scalar3& tilt) { UP_ASSERT_EQUAL(exec_conf->getNRanks(), 8); + auto ref_box = std::make_shared(5.0); + auto box = std::make_shared(L); + box->setTiltFactors(tilt.x, tilt.y, tilt.z); + bool is_orthorhombic = tilt.x == Scalar(0.0) && tilt.y == Scalar(0.0) && tilt.z == Scalar(0.0); + std::shared_ptr> snap(new SnapshotSystemData()); - snap->global_box = std::make_shared(5.0); + snap->global_box = box; snap->particle_data.type_mapping.push_back("A"); // dummy initialize one particle to every domain, we will move them outside the domains for // the tests @@ -968,14 +1024,14 @@ template void celllist_edge_test(std::shared_ptrmpcd_data.resize(8); snap->mpcd_data.type_mapping.push_back("A"); - snap->mpcd_data.position[0] = vec3(-1.0, -1.0, -1.0); - snap->mpcd_data.position[1] = vec3(1.0, -1.0, -1.0); - snap->mpcd_data.position[2] = vec3(-1.0, 1.0, -1.0); - snap->mpcd_data.position[3] = vec3(1.0, 1.0, -1.0); - snap->mpcd_data.position[4] = vec3(-1.0, -1.0, 1.0); - snap->mpcd_data.position[5] = vec3(1.0, -1.0, 1.0); - snap->mpcd_data.position[6] = vec3(-1.0, 1.0, 1.0); - snap->mpcd_data.position[7] = vec3(1.0, 1.0, 1.0); + snap->mpcd_data.position[0] = scale(vec3(-1.0, -1.0, -1.0), ref_box, box); + snap->mpcd_data.position[1] = scale(vec3(1.0, -1.0, -1.0), ref_box, box); + snap->mpcd_data.position[2] = scale(vec3(-1.0, 1.0, -1.0), ref_box, box); + snap->mpcd_data.position[3] = scale(vec3(1.0, 1.0, -1.0), ref_box, box); + snap->mpcd_data.position[4] = scale(vec3(-1.0, -1.0, 1.0), ref_box, box); + snap->mpcd_data.position[5] = scale(vec3(1.0, -1.0, 1.0), ref_box, box); + snap->mpcd_data.position[6] = scale(vec3(-1.0, 1.0, 1.0), ref_box, box); + snap->mpcd_data.position[7] = scale(vec3(1.0, 1.0, 1.0), ref_box, box); std::vector fx {0.5}; std::vector fy {0.45}; std::vector fz {0.55}; @@ -986,7 +1042,7 @@ template void celllist_edge_test(std::shared_ptrsetCommunicator(pdata_comm); std::shared_ptr pdata = sysdef->getMPCDParticleData(); - std::shared_ptr cl(new CL(sysdef, 1.0, false)); + std::shared_ptr cl(new CL(sysdef, make_uint3(5, 5, 5), false)); // move particles to edges of domains for testing const unsigned int my_rank = exec_conf->getRank(); @@ -997,212 +1053,147 @@ template void celllist_edge_test(std::shared_ptrcompute(0); - + checkDomainBoundaries(sysdef, cl); { ArrayHandle h_cell_np(cl->getCellSizeArray(), access_location::host, access_mode::read); - ArrayHandle h_cell_list(cl->getCellList(), - access_location::host, - access_mode::read); - Index3D ci = cl->getCellIndexer(); ArrayHandle h_vel(pdata->getVelocities(), access_location::host, access_mode::read); - - switch (my_rank) - { - case 0: - // global index is (2,2,2), with origin (-1,-1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(3, 3, 3)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(3, 3, 3)); - break; - case 1: - // global index is (2,2,2), with origin (2,-1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 3, 3)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 3, 3)); - break; - case 2: - // global index is (2,2,2), with origin (-1,1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(3, 1, 3)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(3, 1, 3)); - break; - case 3: - // global index is (2,2,2), with origin (2,1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 1, 3)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 1, 3)); - break; - case 4: - // global index is (2,2,2), with origin (-1,-1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(3, 3, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(3, 3, 0)); - break; - case 5: - // global index is (2,2,2), with origin (2,-1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 3, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 3, 0)); - break; - case 6: - // global index is (2,2,2), with origin (-1,1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(3, 1, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(3, 1, 0)); - break; - case 7: - // global index is (2,2,2), with origin (2,1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 1, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 1, 0)); - break; - }; + const unsigned int local_cell = make_local_cell(cl, 2, 2, 2); + UP_ASSERT_EQUAL(h_cell_np.data[local_cell], 1); + UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), local_cell); } // apply a grid shift, particles on left internal boundary will move up one cell // particles on right internal boundary will stay in the same cell - cl->setGridShift(make_scalar3(-0.5, -0.5, -0.5)); - cl->compute(1); + const Scalar3 shift = (Scalar(0.5) / 5) * make_scalar3(1, 1, 1); { + cl->setGridShift(-shift); + cl->compute(1); + checkDomainBoundaries(sysdef, cl); ArrayHandle h_cell_np(cl->getCellSizeArray(), access_location::host, access_mode::read); - ArrayHandle h_cell_list(cl->getCellList(), - access_location::host, - access_mode::read); - Index3D ci = cl->getCellIndexer(); ArrayHandle h_vel(pdata->getVelocities(), access_location::host, access_mode::read); + int3 cell; switch (my_rank) { case 0: - // global index is (2,2,2), with origin (-1,-1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(3, 3, 3)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(3, 3, 3)); + cell = make_int3(2, 2, 2); break; case 1: - // global index is (3,2,2), with origin (2,-1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(1, 3, 3)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(1, 3, 3)); + cell = make_int3(3, 2, 2); break; case 2: - // global index is (2,3,2), with origin (-1,1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(3, 2, 3)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(3, 2, 3)); + cell = make_int3(2, 3, 2); break; case 3: - // global index is (3,3,2), with origin (2,1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(1, 2, 3)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(1, 2, 3)); + cell = make_int3(3, 3, 2); break; case 4: - // global index is (2,2,3), with origin (-1,-1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(3, 3, 1)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(3, 3, 1)); + cell = make_int3(2, 2, 3); break; case 5: - // global index is (3,2,3), with origin (2,-1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(1, 3, 1)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(1, 3, 1)); + cell = make_int3(3, 2, 3); break; case 6: - // global index is (2,3,3), with origin (-1,1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(3, 2, 1)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(3, 2, 1)); + cell = make_int3(2, 3, 3); break; case 7: - // global index is (3,3,3), with origin (2,1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(1, 2, 1)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(1, 2, 1)); + cell = make_int3(3, 3, 3); break; }; + + const unsigned int local_cell = make_local_cell(cl, cell.x, cell.y, cell.z); + UP_ASSERT_EQUAL(h_cell_np.data[local_cell], 1); + UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), local_cell); } - // apply a grid shift, particles on left internal boundary will stay in cell - // particles on right internal boundary will move down one cell - cl->setGridShift(make_scalar3(0.5, 0.5, 0.5)); - cl->compute(2); + // apply a grid shift, particles on left internal boundary will stay in cell + // particles on right internal boundary will move down one cell + // if (*box == *ref_box) { + cl->setGridShift(shift); + cl->compute(2); + checkDomainBoundaries(sysdef, cl); + ArrayHandle h_cell_np(cl->getCellSizeArray(), access_location::host, access_mode::read); - ArrayHandle h_cell_list(cl->getCellList(), - access_location::host, - access_mode::read); - Index3D ci = cl->getCellIndexer(); ArrayHandle h_vel(pdata->getVelocities(), access_location::host, access_mode::read); + int3 cell; switch (my_rank) { case 0: - // global index is (1,1,1), with origin (-1,-1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(2, 2, 2)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(2, 2, 2)); + cell = make_int3(1, 1, 1); break; case 1: - // global index is (2,1,1), with origin (2,-1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 2, 2)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 2, 2)); + cell = make_int3(2, 1, 1); break; case 2: - // global index is (1,2,1), with origin (-1,1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(2, 1, 2)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(2, 1, 2)); + cell = make_int3(1, 2, 1); break; case 3: - // global index is (2,2,1), with origin (2,1,-1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 1, 2)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 1, 2)); + cell = make_int3(2, 2, 1); break; case 4: - // global index is (1,1,2), with origin (-1,-1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(2, 2, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(2, 2, 0)); + cell = make_int3(1, 1, 2); break; case 5: - // global index is (2,1,2), with origin (2,-1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 2, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 2, 0)); + cell = make_int3(2, 1, 2); break; case 6: - // global index is (1,2,2), with origin (-1,1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(2, 1, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(2, 1, 0)); + cell = make_int3(1, 2, 2); break; case 7: - // global index is (2,2,2), with origin (2,1,2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 1, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 1, 0)); + cell = make_int3(2, 2, 2); break; }; + + const unsigned int local_cell = make_local_cell(cl, cell.x, cell.y, cell.z); + UP_ASSERT_EQUAL(h_cell_np.data[local_cell], 1); + UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), local_cell); } + // now we move the particles to their exterior boundaries, and repeat the testing process // we are going to pad the cell list with an extra cell just to test that binning now cl->setNExtraCells(1); @@ -1213,28 +1204,28 @@ template void celllist_edge_test(std::shared_ptr void celllist_edge_test(std::shared_ptrsetGridShift(make_scalar3(0, 0, 0)); cl->compute(3); + checkDomainBoundaries(sysdef, cl); { ArrayHandle h_cell_np(cl->getCellSizeArray(), access_location::host, access_mode::read); - ArrayHandle h_cell_list(cl->getCellList(), - access_location::host, - access_mode::read); - Index3D ci = cl->getCellIndexer(); ArrayHandle h_vel(pdata->getVelocities(), access_location::host, access_mode::read); + int3 cell; switch (my_rank) { case 0: - // global index is (-2,-2,-2), with origin (-2,-2,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 0, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 0, 0)); + cell = make_int3(-2, -2, -2); break; case 1: - // global index is (6,-2,-2), with origin (1,-2,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(5, 0, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(5, 0, 0)); + cell = make_int3(6, -2, -2); break; case 2: - // global index is (-2,6,-2), with origin (-2,0,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 6, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 6, 0)); + cell = make_int3(-2, 6, -2); break; case 3: - // global index is (6,6,-2), with origin (1,0,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(5, 6, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(5, 6, 0)); + cell = make_int3(6, 6, -2); break; case 4: - // global index is (-2,-2,6), with origin (-2,-2,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 0, 5)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 0, 5)); + cell = make_int3(-2, -2, 6); break; case 5: - // global index is (6,-2,6), with origin (1,-2,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(5, 0, 5)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(5, 0, 5)); + cell = make_int3(6, -2, 6); break; case 6: - // global index is (-2,6,6), with origin (-2,0,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 6, 5)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 6, 5)); + cell = make_int3(-2, 6, 6); break; case 7: - // global index is (6,6,6), with origin (1,0,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(5, 6, 5)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(5, 6, 5)); + cell = make_int3(6, 6, 6); break; }; + + const unsigned int local_cell = make_local_cell(cl, cell.x, cell.y, cell.z); + UP_ASSERT_EQUAL(h_cell_np.data[local_cell], 1); + UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), local_cell); } // shift all particles to the right by 0.5 // all particles on left bound will move up one cell, all particles on right bound stay - cl->setGridShift(make_scalar3(-0.5, -0.5, -0.5)); - cl->compute(4); + // this test has weird round off issues for triclinic, so only run for orthorhombic boxes + if (is_orthorhombic) { + cl->setGridShift(-shift); + cl->compute(4); + checkDomainBoundaries(sysdef, cl); + ArrayHandle h_cell_np(cl->getCellSizeArray(), access_location::host, access_mode::read); - ArrayHandle h_cell_list(cl->getCellList(), - access_location::host, - access_mode::read); - Index3D ci = cl->getCellIndexer(); ArrayHandle h_vel(pdata->getVelocities(), access_location::host, access_mode::read); + int3 cell; switch (my_rank) { case 0: - // global index is (-1,-1,-1), with origin (-2,-2,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(1, 1, 1)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(1, 1, 1)); + cell = make_int3(-2, -2, -2); break; case 1: - // global index is (6,-1,-1), with origin (1,-2,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(5, 1, 1)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(5, 1, 1)); + cell = make_int3(6, -2, -2); break; case 2: - // global index is (-1,6,-1), with origin (-2,0,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(1, 6, 1)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(1, 6, 1)); + cell = make_int3(-2, 6, -2); break; case 3: - // global index is (6,6,-1), with origin (1,0,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(5, 6, 1)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(5, 6, 1)); + cell = make_int3(6, 6, -2); break; case 4: - // global index is (-1,-1,6), with origin (-2,-2,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(1, 1, 5)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(1, 1, 5)); + cell = make_int3(-2, -2, 6); break; case 5: - // global index is (6,-1,6), with origin (1,-2,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(5, 1, 5)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(5, 1, 5)); + cell = make_int3(6, -2, 6); break; case 6: - // global index is (-1,6,6), with origin (-2,0,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(1, 6, 5)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(1, 6, 5)); + cell = make_int3(-2, 6, 6); break; case 7: - // global index is (6,6,6), with origin (1,0,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(5, 6, 5)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(5, 6, 5)); + cell = make_int3(6, 6, 6); break; }; + + const unsigned int local_cell = make_local_cell(cl, cell.x, cell.y, cell.z); + UP_ASSERT_EQUAL(h_cell_np.data[local_cell], 1); + UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), local_cell); } - // shift all particles left by 0.5 - // particles on the lower bound stay in the same bin, and particles on the right bound move down - // one - cl->setGridShift(make_scalar3(0.5, 0.5, 0.5)); - cl->compute(5); + // shift all particles left by 0.5 + // particles on the lower bound stay in the same bin, and particles on the right bound move + // down one { + cl->setGridShift(shift); + cl->compute(5); + checkDomainBoundaries(sysdef, cl); + ArrayHandle h_cell_np(cl->getCellSizeArray(), access_location::host, access_mode::read); - ArrayHandle h_cell_list(cl->getCellList(), - access_location::host, - access_mode::read); - Index3D ci = cl->getCellIndexer(); ArrayHandle h_vel(pdata->getVelocities(), access_location::host, access_mode::read); + int3 cell; switch (my_rank) { case 0: - // global index is (-2,-2,-2), with origin (-2,-2,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 0, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 0, 0)); + cell = make_int3(-2, -2, -2); break; case 1: - // global index is (5,-2,-2), with origin (1,-2,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(4, 0, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(4, 0, 0)); + cell = make_int3(5, -2, -2); break; case 2: - // global index is (-2,5,-2), with origin (-2,0,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 5, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 5, 0)); + cell = make_int3(-2, 5, -2); break; case 3: - // global index is (5,5,-2), with origin (1,0,-2) - UP_ASSERT_EQUAL(h_cell_np.data[ci(4, 5, 0)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(4, 5, 0)); + cell = make_int3(5, 5, -2); break; case 4: - // global index is (-2,-2,5), with origin (-2,-2,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 0, 4)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 0, 4)); + cell = make_int3(-2, -2, 5); break; case 5: - // global index is (5,-2,5), with origin (1,-2,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(4, 0, 4)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(4, 0, 4)); + cell = make_int3(5, -2, 5); break; case 6: - // global index is (-2,5,5), with origin (-2,0,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(0, 5, 4)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(0, 5, 4)); + cell = make_int3(-2, 5, 5); break; case 7: - // global index is (5,5,5), with origin (1,0,1) - UP_ASSERT_EQUAL(h_cell_np.data[ci(4, 5, 4)], 1); - UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), ci(4, 5, 4)); + cell = make_int3(5, 5, 5); break; }; + + const unsigned int local_cell = make_local_cell(cl, cell.x, cell.y, cell.z); + UP_ASSERT_EQUAL(h_cell_np.data[local_cell], 1); + UP_ASSERT_EQUAL(__scalar_as_int(h_vel.data[0].w), local_cell); } } @@ -1431,40 +1384,159 @@ UP_TEST(mpcd_cell_list_dimensions) std::shared_ptr exec_conf( new ExecutionConfiguration(ExecutionConfiguration::CPU)); exec_conf->getMPIConfig()->splitPartitions(2); - celllist_dimension_test(exec_conf, true, false, false); - celllist_dimension_test(exec_conf, false, true, false); - celllist_dimension_test(exec_conf, false, false, true); + celllist_dimension_test(exec_conf, + true, + false, + false, + make_scalar3(0, 0, 0)); + celllist_dimension_test(exec_conf, + false, + true, + false, + make_scalar3(0, 0, 0)); + celllist_dimension_test(exec_conf, + false, + false, + true, + make_scalar3(0, 0, 0)); } // mpi in 2d { std::shared_ptr exec_conf( new ExecutionConfiguration(ExecutionConfiguration::CPU)); exec_conf->getMPIConfig()->splitPartitions(4); - celllist_dimension_test(exec_conf, true, true, false); - celllist_dimension_test(exec_conf, true, false, true); - celllist_dimension_test(exec_conf, false, true, true); + celllist_dimension_test(exec_conf, + true, + true, + false, + make_scalar3(0, 0, 0)); + celllist_dimension_test(exec_conf, + true, + false, + true, + make_scalar3(0, 0, 0)); + celllist_dimension_test(exec_conf, + false, + true, + true, + make_scalar3(0, 0, 0)); } // mpi in 3d { std::shared_ptr exec_conf( new ExecutionConfiguration(ExecutionConfiguration::CPU)); exec_conf->getMPIConfig()->splitPartitions(8); - celllist_dimension_test(exec_conf, true, true, true); + celllist_dimension_test(exec_conf, true, true, true, make_scalar3(0, 0, 0)); + } + } + +//! dimension test case for MPCD CellList class, triclinic +UP_TEST(mpcd_cell_list_dimensions_triclinic) + { + // mpi in 1d + { + auto exec_conf = std::make_shared(ExecutionConfiguration::CPU); + exec_conf->getMPIConfig()->splitPartitions(2); + celllist_dimension_test(exec_conf, + true, + false, + false, + make_scalar3(0.5, -0.75, 1.0)); + celllist_dimension_test(exec_conf, + false, + true, + false, + make_scalar3(0.5, -0.75, 1.0)); + celllist_dimension_test(exec_conf, + false, + false, + true, + make_scalar3(0.5, -0.75, 1.0)); + } + // mpi in 2d + { + auto exec_conf = std::make_shared(ExecutionConfiguration::CPU); + exec_conf->getMPIConfig()->splitPartitions(4); + celllist_dimension_test(exec_conf, + true, + true, + false, + make_scalar3(0.5, -0.75, 1.0)); + celllist_dimension_test(exec_conf, + true, + false, + true, + make_scalar3(0.5, -0.75, 1.0)); + celllist_dimension_test(exec_conf, + false, + true, + true, + make_scalar3(0.5, -0.75, 1.0)); + } + // mpi in 3d + { + auto exec_conf = std::make_shared(ExecutionConfiguration::CPU); + exec_conf->getMPIConfig()->splitPartitions(8); + celllist_dimension_test(exec_conf, + true, + true, + true, + make_scalar3(0.5, -0.75, 1.0)); } } //! basic test case for MPCD CellList class UP_TEST(mpcd_cell_list_basic_test) { - celllist_basic_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::CPU))); + celllist_basic_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.0, 6.0, 6.0), + make_scalar3(0, 0, 0)); + } + +//! basic test case for MPCD CellList class, noncubic +UP_TEST(mpcd_cell_list_basic_test_noncubic) + { + celllist_basic_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.5, 7.0, 7.5), + make_scalar3(0, 0, 0)); + } + +//! basic test case for MPCD CellList class, triclinic +UP_TEST(mpcd_cell_list_basic_test_triclinic) + { + celllist_basic_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.0, 6.0, 6.0), + make_scalar3(0.5, -0.75, 1.0)); } //! edge test case for MPCD CellList class UP_TEST(mpcd_cell_list_edge_test) { - celllist_edge_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::CPU))); + celllist_edge_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(5.0, 5.0, 5.0), + make_scalar3(0, 0, 0)); + } + +//! edge test case for MPCD CellList class, noncubic +UP_TEST(mpcd_cell_list_edge_test_noncubic) + { + celllist_edge_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.0, 6.5, 7.0), + make_scalar3(0, 0, 0)); + } + +//! edge test case for MPCD CellList class, triclinic +UP_TEST(mpcd_cell_list_edge_test_triclinic) + { + celllist_edge_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(5.0, 5.0, 5.0), + make_scalar3(0.5, -0.75, 1.0)); } #ifdef ENABLE_HIP @@ -1476,39 +1548,162 @@ UP_TEST(mpcd_cell_list_gpu_dimensions) std::shared_ptr exec_conf( new ExecutionConfiguration(ExecutionConfiguration::GPU)); exec_conf->getMPIConfig()->splitPartitions(2); - celllist_dimension_test(exec_conf, true, false, false); - celllist_dimension_test(exec_conf, false, true, false); - celllist_dimension_test(exec_conf, false, false, true); + celllist_dimension_test(exec_conf, + true, + false, + false, + make_scalar3(0, 0, 0)); + celllist_dimension_test(exec_conf, + false, + true, + false, + make_scalar3(0, 0, 0)); + celllist_dimension_test(exec_conf, + false, + false, + true, + make_scalar3(0, 0, 0)); } // mpi in 2d { std::shared_ptr exec_conf( new ExecutionConfiguration(ExecutionConfiguration::GPU)); exec_conf->getMPIConfig()->splitPartitions(4); - celllist_dimension_test(exec_conf, true, true, false); - celllist_dimension_test(exec_conf, true, false, true); - celllist_dimension_test(exec_conf, false, true, true); + celllist_dimension_test(exec_conf, + true, + true, + false, + make_scalar3(0, 0, 0)); + celllist_dimension_test(exec_conf, + true, + false, + true, + make_scalar3(0, 0, 0)); + celllist_dimension_test(exec_conf, + false, + true, + true, + make_scalar3(0, 0, 0)); } // mpi in 3d { std::shared_ptr exec_conf( new ExecutionConfiguration(ExecutionConfiguration::GPU)); exec_conf->getMPIConfig()->splitPartitions(8); - celllist_dimension_test(exec_conf, true, true, true); + celllist_dimension_test(exec_conf, + true, + true, + true, + make_scalar3(0, 0, 0)); + } + } + +//! dimension test case for MPCD CellListGPU class +UP_TEST(mpcd_cell_list_gpu_dimensions_triclinic) + { + // mpi in 1d + { + auto exec_conf = std::make_shared(ExecutionConfiguration::GPU); + exec_conf->getMPIConfig()->splitPartitions(2); + celllist_dimension_test(exec_conf, + true, + false, + false, + make_scalar3(0.5, -0.75, 1.0)); + celllist_dimension_test(exec_conf, + false, + true, + false, + make_scalar3(0.5, -0.75, 1.0)); + celllist_dimension_test(exec_conf, + false, + false, + true, + make_scalar3(0.5, -0.75, 1.0)); + } + // mpi in 2d + { + auto exec_conf = std::make_shared(ExecutionConfiguration::GPU); + exec_conf->getMPIConfig()->splitPartitions(4); + celllist_dimension_test(exec_conf, + true, + true, + false, + make_scalar3(0.5, -0.75, 1.0)); + celllist_dimension_test(exec_conf, + true, + false, + true, + make_scalar3(0.5, -0.75, 1.0)); + celllist_dimension_test(exec_conf, + false, + true, + true, + make_scalar3(0.5, -0.75, 1.0)); + } + // mpi in 3d + { + auto exec_conf = std::make_shared(ExecutionConfiguration::GPU); + exec_conf->getMPIConfig()->splitPartitions(8); + celllist_dimension_test(exec_conf, + true, + true, + true, + make_scalar3(0.5, -0.75, 1.0)); } } //! basic test case for MPCD CellListGPU class UP_TEST(mpcd_cell_list_gpu_basic_test) { - celllist_basic_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::GPU))); + celllist_basic_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.0, 6.0, 6.0), + make_scalar3(0, 0, 0)); + } + +//! basic test case for MPCD CellListGPU class, noncubic +UP_TEST(mpcd_cell_list_gpu_basic_test_noncubic) + { + celllist_basic_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.5, 7.0, 7.5), + make_scalar3(0, 0, 0)); + } + +//! basic test case for MPCD CellListGPU class, triclinic +UP_TEST(mpcd_cell_list_gpu_basic_test_triclinic) + { + celllist_basic_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.0, 6.0, 6.0), + make_scalar3(0.5, -0.75, 1.0)); } //! edge test case for MPCD CellListGPU class UP_TEST(mpcd_cell_list_gpu_edge_test) { - celllist_edge_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::GPU))); + celllist_edge_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(5.0, 5.0, 5.0), + make_scalar3(0, 0, 0)); + } + +//! edge test case for MPCD CellListGPU class, noncubic +UP_TEST(mpcd_cell_list_gpu_edge_test_noncubic) + { + celllist_edge_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.0, 6.5, 7.0), + make_scalar3(0, 0, 0)); + } + +//! edge test case for MPCD CellListGPU class, triclinic +UP_TEST(mpcd_cell_list_gpu_edge_test_triclinic) + { + celllist_edge_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(5.0, 5.0, 5.0), + make_scalar3(0.5, -0.75, 1.0)); } #endif // ENABLE_HIP diff --git a/hoomd/mpcd/test/cell_list_test.cc b/hoomd/mpcd/test/cell_list_test.cc index b0c3e22017..0d96bdd458 100644 --- a/hoomd/mpcd/test/cell_list_test.cc +++ b/hoomd/mpcd/test/cell_list_test.cc @@ -11,15 +11,21 @@ #include "hoomd/filter/ParticleFilterType.h" #include "hoomd/test/upp11_config.h" +#include "utils.h" + HOOMD_UP_MAIN() using namespace hoomd; //! Test for correct calculation of MPCD grid dimensions -template void celllist_dimension_test(std::shared_ptr exec_conf) +template +void celllist_dimension_test(std::shared_ptr exec_conf, + const Scalar3& L, + const Scalar3& tilt) { std::shared_ptr> snap(new SnapshotSystemData()); - snap->global_box = std::make_shared(6.0, 8.0, 10.0); + snap->global_box = std::make_shared(L); + snap->global_box->setTiltFactors(tilt.x, tilt.y, tilt.z); snap->particle_data.type_mapping.push_back("A"); snap->mpcd_data.resize(1); snap->mpcd_data.type_mapping.push_back("A"); @@ -28,7 +34,7 @@ template void celllist_dimension_test(std::shared_ptrgetMPCDParticleData(); // define a system of different edge lengths - std::shared_ptr cl(new CL(sysdef, 1.0, false)); + std::shared_ptr cl(new CL(sysdef, make_uint3(6, 8, 10), false)); // compute the cell list dimensions cl->computeDimensions(); @@ -57,7 +63,7 @@ template void celllist_dimension_test(std::shared_ptrsetCellSize(2.0); + cl->setGlobalDim(make_uint3(3, 4, 5)); cl->computeDimensions(); dim = cl->getDim(); @@ -76,46 +82,38 @@ template void celllist_dimension_test(std::shared_ptrgetCellList().getNumElements() >= 3 * 4 * 5 * Nmax); - - /*******************/ - // Change the cell size to something that does not evenly divide a side, and check for an - // exception evenly divides no sides - cl->setCellSize(4.2); - UP_ASSERT_EXCEPTION(std::runtime_error, [&] { cl->computeDimensions(); }); - // evenly divides z - cl->setCellSize(10.0); - UP_ASSERT_EXCEPTION(std::runtime_error, [&] { cl->computeDimensions(); }); - // evenly divides y - cl->setCellSize(8.0); - UP_ASSERT_EXCEPTION(std::runtime_error, [&] { cl->computeDimensions(); }); - // evenly divides x - cl->setCellSize(6.0); - UP_ASSERT_EXCEPTION(std::runtime_error, [&] { cl->computeDimensions(); }); } //! Test for correct cell listing of a small system -template void celllist_small_test(std::shared_ptr exec_conf) +template +void celllist_small_test(std::shared_ptr exec_conf, + const Scalar3& L, + const Scalar3& tilt) { + auto ref_box = std::make_shared(2.0); + auto box = std::make_shared(L); + box->setTiltFactors(tilt.x, tilt.y, tilt.z); + std::shared_ptr> snap(new SnapshotSystemData()); - snap->global_box = std::make_shared(2.0); + snap->global_box = box; snap->particle_data.type_mapping.push_back("A"); // place each particle in a different cell, doubling the first cell snap->mpcd_data.resize(9); snap->mpcd_data.type_mapping.push_back("A"); - snap->mpcd_data.position[0] = vec3(-0.5, -0.5, -0.5); - snap->mpcd_data.position[1] = vec3(0.5, -0.5, -0.5); - snap->mpcd_data.position[2] = vec3(-0.5, 0.5, -0.5); - snap->mpcd_data.position[3] = vec3(0.5, 0.5, -0.5); - snap->mpcd_data.position[4] = vec3(-0.5, -0.5, 0.5); - snap->mpcd_data.position[5] = vec3(0.5, -0.5, 0.5); - snap->mpcd_data.position[6] = vec3(-0.5, 0.5, 0.5); - snap->mpcd_data.position[7] = vec3(0.5, 0.5, 0.5); - snap->mpcd_data.position[8] = vec3(-0.5, -0.5, -0.5); + snap->mpcd_data.position[0] = scale(vec3(-0.5, -0.5, -0.5), ref_box, box); + snap->mpcd_data.position[1] = scale(vec3(0.5, -0.5, -0.5), ref_box, box); + snap->mpcd_data.position[2] = scale(vec3(-0.5, 0.5, -0.5), ref_box, box); + snap->mpcd_data.position[3] = scale(vec3(0.5, 0.5, -0.5), ref_box, box); + snap->mpcd_data.position[4] = scale(vec3(-0.5, -0.5, 0.5), ref_box, box); + snap->mpcd_data.position[5] = scale(vec3(0.5, -0.5, 0.5), ref_box, box); + snap->mpcd_data.position[6] = scale(vec3(-0.5, 0.5, 0.5), ref_box, box); + snap->mpcd_data.position[7] = scale(vec3(0.5, 0.5, 0.5), ref_box, box); + snap->mpcd_data.position[8] = scale(vec3(-0.5, -0.5, -0.5), ref_box, box); std::shared_ptr sysdef(new SystemDefinition(snap, exec_conf)); std::shared_ptr pdata_9 = sysdef->getMPCDParticleData(); - std::shared_ptr cl(new CL(sysdef, 1.0, false)); + std::shared_ptr cl(new CL(sysdef, make_uint3(2, 2, 2), false)); cl->compute(0); // check that each particle is in the proper bin (cell list and velocity) @@ -170,8 +168,8 @@ template void celllist_small_test(std::shared_ptr h_pos(pdata_9->getPositions(), access_location::host, access_mode::overwrite); - h_pos.data[0] = make_scalar4(-0.3, -0.3, -0.3, 0.0); - h_pos.data[1] = make_scalar4(0.3, 0.3, 0.3, 0.0); + h_pos.data[0] = scale(make_scalar4(-0.3, -0.3, -0.3, __int_as_scalar(0)), ref_box, box); + h_pos.data[1] = scale(make_scalar4(0.3, 0.3, 0.3, __int_as_scalar(0)), ref_box, box); h_pos.data[2] = h_pos.data[0]; h_pos.data[3] = h_pos.data[1]; h_pos.data[4] = h_pos.data[0]; @@ -233,7 +231,7 @@ template void celllist_small_test(std::shared_ptr h_pos(pdata_9->getPositions(), access_location::host, access_mode::overwrite); - h_pos.data[0] = make_scalar4(0.9, -0.4, 0.0, 0.0); + h_pos.data[0] = scale(make_scalar4(0.9, -0.4, 0.0, __int_as_scalar(0)), ref_box, box); for (unsigned int i = 1; i < 9; ++i) h_pos.data[i] = h_pos.data[0]; } @@ -260,7 +258,7 @@ template void celllist_small_test(std::shared_ptr h_pos(pdata_9->getPositions(), access_location::host, access_mode::overwrite); - h_pos.data[0] = make_scalar4(2.1, 2.1, 2.1, __int_as_scalar(0)); + h_pos.data[0] = scale(make_scalar4(2.1, 2.1, 2.1, __int_as_scalar(0)), ref_box, box); } UP_ASSERT_EXCEPTION(std::runtime_error, [&] { cl->compute(3); }); // check the other side as well @@ -268,24 +266,31 @@ template void celllist_small_test(std::shared_ptr h_pos(pdata_9->getPositions(), access_location::host, access_mode::overwrite); - h_pos.data[0] = make_scalar4(-2.1, -2.1, -2.1, __int_as_scalar(0)); + h_pos.data[0] = scale(make_scalar4(-2.1, -2.1, -2.1, __int_as_scalar(0)), ref_box, box); } UP_ASSERT_EXCEPTION(std::runtime_error, [&] { cl->compute(4); }); } //! Test that particles can be grid shifted correctly -template void celllist_grid_shift_test(std::shared_ptr exec_conf) +template +void celllist_grid_shift_test(std::shared_ptr exec_conf, + const Scalar3& L, + const Scalar3& tilt) { + auto ref_box = std::make_shared(6.0); + auto box = std::make_shared(L); + box->setTiltFactors(tilt.x, tilt.y, tilt.z); + std::shared_ptr> snap(new SnapshotSystemData()); - snap->global_box = std::make_shared(6.0); + snap->global_box = box; snap->particle_data.type_mapping.push_back("A"); snap->mpcd_data.resize(1); snap->mpcd_data.type_mapping.push_back("A"); - snap->mpcd_data.position[0] = vec3(0.1, 0.1, 0.1); + snap->mpcd_data.position[0] = scale(vec3(0.1, 0.1, 0.1), ref_box, box); std::shared_ptr sysdef(new SystemDefinition(snap, exec_conf)); std::shared_ptr pdata_1 = sysdef->getMPCDParticleData(); - std::shared_ptr cl(new CL(sysdef, 1.0, false)); + std::shared_ptr cl(new CL(sysdef, make_uint3(6, 6, 6), false)); cl->compute(0); { ArrayHandle h_cell_np(cl->getCellSizeArray(), @@ -296,7 +301,8 @@ template void celllist_grid_shift_test(std::shared_ptrsetGridShift(make_scalar3(0.5, 0.5, 0.5)); + const Scalar3 shift = (Scalar(0.5) / 6) * make_scalar3(1, 1, 1); + cl->setGridShift(shift); cl->compute(1); { ArrayHandle h_cell_np(cl->getCellSizeArray(), @@ -311,9 +317,9 @@ template void celllist_grid_shift_test(std::shared_ptr h_pos(pdata_1->getPositions(), access_location::host, access_mode::overwrite); - h_pos.data[0] = make_scalar4(-0.1, -0.1, -0.1, 0.0); + h_pos.data[0] = scale(make_scalar4(-0.1, -0.1, -0.1, __int_as_scalar(0)), ref_box, box); } - cl->setGridShift(make_scalar3(-0.5, -0.5, -0.5)); + cl->setGridShift(-shift); cl->compute(2); { ArrayHandle h_cell_np(cl->getCellSizeArray(), @@ -328,9 +334,9 @@ template void celllist_grid_shift_test(std::shared_ptr h_pos(pdata_1->getPositions(), access_location::host, access_mode::overwrite); - h_pos.data[0] = make_scalar4(-2.9, -2.9, -2.9, 0.0); + h_pos.data[0] = scale(make_scalar4(-2.9, -2.9, -2.9, __int_as_scalar(0)), ref_box, box); } - cl->setGridShift(make_scalar3(0.5, 0.5, 0.5)); + cl->setGridShift(shift); cl->compute(3); { ArrayHandle h_cell_np(cl->getCellSizeArray(), @@ -345,9 +351,9 @@ template void celllist_grid_shift_test(std::shared_ptr h_pos(pdata_1->getPositions(), access_location::host, access_mode::overwrite); - h_pos.data[0] = make_scalar4(2.9, 2.9, 2.9, 0.0); + h_pos.data[0] = scale(make_scalar4(2.9, 2.9, 2.9, __int_as_scalar(0)), ref_box, box); } - cl->setGridShift(make_scalar3(-0.5, -0.5, -0.5)); + cl->setGridShift(-shift); cl->compute(4); { ArrayHandle h_cell_np(cl->getCellSizeArray(), @@ -358,31 +364,36 @@ template void celllist_grid_shift_test(std::shared_ptrsetGridShift(make_scalar3(-0.51, -0.51, -0.51)); }); - UP_ASSERT_EXCEPTION(std::runtime_error, - [&] { cl->setGridShift(make_scalar3(0.51, 0.51, 0.51)); }); + UP_ASSERT_EXCEPTION(std::runtime_error, [&] { cl->setGridShift(Scalar(-1.01) * shift); }); + UP_ASSERT_EXCEPTION(std::runtime_error, [&] { cl->setGridShift(Scalar(1.01) * shift); }); } //! Test that small systems can embed particles -template void celllist_embed_test(std::shared_ptr exec_conf) +template +void celllist_embed_test(std::shared_ptr exec_conf, + const Scalar3& L, + const Scalar3& tilt) { + auto ref_box = std::make_shared(2.0); + auto box = std::make_shared(L); + box->setTiltFactors(tilt.x, tilt.y, tilt.z); + // setup a system where both MD and MPCD particles are in each of the cells std::shared_ptr> snap(new SnapshotSystemData()); - snap->global_box = std::make_shared(2.0); + snap->global_box = box; { SnapshotParticleData& pdata_snap = snap->particle_data; pdata_snap.type_mapping.push_back("A"); pdata_snap.type_mapping.push_back("B"); pdata_snap.resize(8); - pdata_snap.pos[0] = vec3(-0.5, -0.5, -0.5); - pdata_snap.pos[1] = vec3(0.5, -0.5, -0.5); - pdata_snap.pos[2] = vec3(-0.5, 0.5, -0.5); - pdata_snap.pos[3] = vec3(0.5, 0.5, -0.5); - pdata_snap.pos[4] = vec3(-0.5, -0.5, 0.5); - pdata_snap.pos[5] = vec3(0.5, -0.5, 0.5); - pdata_snap.pos[6] = vec3(-0.5, 0.5, 0.5); - pdata_snap.pos[7] = vec3(0.5, 0.5, 0.5); + pdata_snap.pos[0] = scale(vec3(-0.5, -0.5, -0.5), ref_box, box); + pdata_snap.pos[1] = scale(vec3(0.5, -0.5, -0.5), ref_box, box); + pdata_snap.pos[2] = scale(vec3(-0.5, 0.5, -0.5), ref_box, box); + pdata_snap.pos[3] = scale(vec3(0.5, 0.5, -0.5), ref_box, box); + pdata_snap.pos[4] = scale(vec3(-0.5, -0.5, 0.5), ref_box, box); + pdata_snap.pos[5] = scale(vec3(0.5, -0.5, 0.5), ref_box, box); + pdata_snap.pos[6] = scale(vec3(-0.5, 0.5, 0.5), ref_box, box); + pdata_snap.pos[7] = scale(vec3(0.5, 0.5, 0.5), ref_box, box); pdata_snap.type[0] = 0; pdata_snap.type[1] = 1; pdata_snap.type[2] = 0; @@ -394,18 +405,18 @@ template void celllist_embed_test(std::shared_ptrmpcd_data.resize(8); snap->mpcd_data.type_mapping.push_back("A"); - snap->mpcd_data.position[0] = vec3(-0.5, -0.5, -0.5); - snap->mpcd_data.position[1] = vec3(0.5, -0.5, -0.5); - snap->mpcd_data.position[2] = vec3(-0.5, 0.5, -0.5); - snap->mpcd_data.position[3] = vec3(0.5, 0.5, -0.5); - snap->mpcd_data.position[4] = vec3(-0.5, -0.5, 0.5); - snap->mpcd_data.position[5] = vec3(0.5, -0.5, 0.5); - snap->mpcd_data.position[6] = vec3(-0.5, 0.5, 0.5); - snap->mpcd_data.position[7] = vec3(0.5, 0.5, 0.5); + snap->mpcd_data.position[0] = scale(vec3(-0.5, -0.5, -0.5), ref_box, box); + snap->mpcd_data.position[1] = scale(vec3(0.5, -0.5, -0.5), ref_box, box); + snap->mpcd_data.position[2] = scale(vec3(-0.5, 0.5, -0.5), ref_box, box); + snap->mpcd_data.position[3] = scale(vec3(0.5, 0.5, -0.5), ref_box, box); + snap->mpcd_data.position[4] = scale(vec3(-0.5, -0.5, 0.5), ref_box, box); + snap->mpcd_data.position[5] = scale(vec3(0.5, -0.5, 0.5), ref_box, box); + snap->mpcd_data.position[6] = scale(vec3(-0.5, 0.5, 0.5), ref_box, box); + snap->mpcd_data.position[7] = scale(vec3(0.5, 0.5, 0.5), ref_box, box); std::shared_ptr sysdef(new SystemDefinition(snap, exec_conf)); std::shared_ptr pdata_8 = sysdef->getMPCDParticleData(); - std::shared_ptr cl(new CL(sysdef, 1.0, false)); + std::shared_ptr cl(new CL(sysdef, make_uint3(2, 2, 2), false)); cl->compute(0); // at first, there is no embedded particle, so everything should just look like the test @@ -560,7 +571,7 @@ template void celllist_embed_test(std::shared_ptr h_embed_pos(embed_pdata->getPositions(), access_location::host, access_mode::overwrite); - h_embed_pos.data[1] = make_scalar4(0.5, 0.5, -0.5, __int_as_scalar(1)); + h_embed_pos.data[1] = scale(make_scalar4(0.5, 0.5, -0.5, __int_as_scalar(1)), ref_box, box); } cl->compute(2); // now there should be a second particle in the cell @@ -654,57 +665,217 @@ template void celllist_embed_test(std::shared_ptr(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::CPU))); + celllist_dimension_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.0, 8.0, 10.0), + make_scalar3(0, 0, 0)); + } + +//! dimension test case for MPCD CellList class, noncubic +UP_TEST(mpcd_cell_list_dimensions_noncubic) + { + celllist_dimension_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(8.5, 10.1, 5.9), + make_scalar3(0, 0, 0)); + } + +//! dimension test case for MPCD CellList class, triclinic +UP_TEST(mpcd_cell_list_dimensions_triclinic) + { + celllist_dimension_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.0, 8.0, 10.0), + make_scalar3(0.5, -0.75, 1.0)); } //! small system test case for MPCD CellList class UP_TEST(mpcd_cell_list_small_test) { - celllist_small_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::CPU))); + celllist_small_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(2.0, 2.0, 2.0), + make_scalar3(0, 0, 0)); } -//! small system test case for MPCD CellList class +//! small system test case for MPCD CellList class, noncubic +UP_TEST(mpcd_cell_list_small_test_noncubic) + { + celllist_small_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(3.1, 4.2, 5.3), + make_scalar3(0, 0, 0)); + } + +//! small system test case for MPCD CellList class, triclinic +UP_TEST(mpcd_cell_list_small_test_triclinic) + { + celllist_small_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(2.0, 2.0, 2.0), + make_scalar3(0.5, -0.75, 1.0)); + } + +//! grid shift test case for MPCD CellList class UP_TEST(mpcd_cell_list_grid_shift_test) { - celllist_grid_shift_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::CPU))); + celllist_grid_shift_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.0, 6.0, 6.0), + make_scalar3(0, 0, 0)); + } + +//! grid shift test case for MPCD CellList class, noncubic +UP_TEST(mpcd_cell_list_grid_shift_test_noncubic) + { + celllist_grid_shift_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.1, 7.2, 8.3), + make_scalar3(0, 0, 0)); + } + +//! grid shift test case for MPCD CellList class, triclinic +UP_TEST(mpcd_cell_list_grid_shift_test_triclinic) + { + celllist_grid_shift_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(6.0, 6.0, 6.0), + make_scalar3(0.5, -0.75, 1.0)); } //! embedded particle test case for MPCD CellList class UP_TEST(mpcd_cell_list_embed_test) { - celllist_embed_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::CPU))); + celllist_embed_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(2.0, 2.0, 2.0), + make_scalar3(0, 0, 0)); + } + +//! embedded particle test case for MPCD CellList class, noncubic +UP_TEST(mpcd_cell_list_embed_test_noncubic) + { + celllist_embed_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(3.1, 4.2, 5.3), + make_scalar3(0, 0, 0)); + } + +//! embedded particle test case for MPCD CellList class, triclinic +UP_TEST(mpcd_cell_list_embed_test_triclinic) + { + celllist_embed_test( + std::make_shared(ExecutionConfiguration::CPU), + make_scalar3(2.0, 2.0, 2.0), + make_scalar3(0.5, -0.75, 1.0)); } #ifdef ENABLE_HIP //! dimension test case for MPCD CellListGPU class UP_TEST(mpcd_cell_list_gpu_dimensions) { - celllist_dimension_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::GPU))); + celllist_dimension_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.0, 8.0, 10.0), + make_scalar3(0, 0, 0)); + } + +//! dimension test case for MPCD CellListGPU class, noncubic +UP_TEST(mpcd_cell_list_gpu_dimensions_noncubic) + { + celllist_dimension_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(8.5, 10.1, 5.9), + make_scalar3(0, 0, 0)); + } + +//! dimension test case for MPCD CellList class, triclinic +UP_TEST(mpcd_cell_list_gpu_dimensions_triclinic) + { + celllist_dimension_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.0, 8.0, 10.0), + make_scalar3(0.5, -0.75, 1.0)); } //! small system test case for MPCD CellListGPU class UP_TEST(mpcd_cell_list_gpu_small_test) { - celllist_small_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::GPU))); + celllist_small_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(2.0, 2.0, 2.0), + make_scalar3(0, 0, 0)); } -//! small system test case for MPCD CellListGPU class +//! small system test case for MPCD CellListGPU class, noncubic +UP_TEST(mpcd_cell_list_gpu_small_test_noncubic) + { + celllist_small_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(3.1, 4.2, 5.3), + make_scalar3(0, 0, 0)); + } + +//! small system test case for MPCD CellListGPU class, triclinic +UP_TEST(mpcd_cell_list_gpu_small_test_triclinic) + { + celllist_small_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(2.0, 2.0, 2.0), + make_scalar3(0.5, -0.75, 1.0)); + } + +//! grid shift test case for MPCD CellListGPU class UP_TEST(mpcd_cell_list_gpu_grid_shift_test) { - celllist_grid_shift_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::GPU))); + celllist_grid_shift_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.0, 6.0, 6.0), + make_scalar3(0, 0, 0)); + } + +//! grid shift test case for MPCD CellListGPU class, noncubic +UP_TEST(mpcd_cell_list_gpu_grid_shift_test_noncubic) + { + celllist_grid_shift_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.1, 7.2, 8.3), + make_scalar3(0, 0, 0)); + } + +//! grid shift test case for MPCD CellListGPU class, triclinic +UP_TEST(mpcd_cell_list_gpu_grid_shift_test_triclinic) + { + celllist_grid_shift_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(6.0, 6.0, 6.0), + make_scalar3(0.5, -0.75, 1.0)); } //! embedded particle test case for MPCD CellListGPU class UP_TEST(mpcd_cell_list_gpu_embed_test) { - celllist_embed_test(std::shared_ptr( - new ExecutionConfiguration(ExecutionConfiguration::GPU))); + celllist_embed_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(2.0, 2.0, 2.0), + make_scalar3(0, 0, 0)); + } + +//! embedded particle test case for MPCD CellListGPU class, noncubic +UP_TEST(mpcd_cell_list_gpu_embed_test_noncubic) + { + celllist_embed_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(3.1, 4.2, 5.3), + make_scalar3(0, 0, 0)); + } + +//! embedded particle test case for MPCD CellListGPU class, triclinic +UP_TEST(mpcd_cell_list_gpu_embed_test_triclinic) + { + celllist_embed_test( + std::make_shared(ExecutionConfiguration::GPU), + make_scalar3(2.0, 2.0, 2.0), + make_scalar3(0.5, -0.75, 1.0)); } #endif // ENABLE_HIP diff --git a/hoomd/mpcd/test/parallel_plate_geometry_filler_test.cc b/hoomd/mpcd/test/parallel_plate_geometry_filler_test.cc index 42b687c618..b450efef2b 100644 --- a/hoomd/mpcd/test/parallel_plate_geometry_filler_test.cc +++ b/hoomd/mpcd/test/parallel_plate_geometry_filler_test.cc @@ -27,7 +27,7 @@ void parallel_plate_fill_basic_test(std::shared_ptr exec std::shared_ptr sysdef(new SystemDefinition(snap, exec_conf)); auto pdata = sysdef->getMPCDParticleData(); - auto cl = std::make_shared(sysdef, 2.0, false); + auto cl = std::make_shared(sysdef, make_uint3(10, 10, 10), false); UP_ASSERT_EQUAL(pdata->getNVirtual(), 0); // create slit channel with half width 5 @@ -111,7 +111,7 @@ void parallel_plate_fill_basic_test(std::shared_ptr exec * Change the cell size so that we lie exactly on a boundary. */ pdata->removeVirtualParticles(); - cl->setCellSize(1.0); + cl->setGlobalDim(make_uint3(20, 20, 20)); filler->fill(2); // volume to fill is now from 5->5.5 on + side, same other parameters UP_ASSERT_EQUAL(pdata->getNVirtual(), 2 * (20 * 20 / 2) * 2); @@ -134,7 +134,7 @@ void parallel_plate_fill_basic_test(std::shared_ptr exec /* * Test the average properties of the virtual particles. */ - cl->setCellSize(2.0); + cl->setGlobalDim(make_uint3(10, 10, 10)); unsigned int N_lo(0), N_hi(0); Scalar3 v_lo = make_scalar3(0, 0, 0); Scalar3 v_hi = make_scalar3(0, 0, 0); diff --git a/hoomd/mpcd/test/planar_pore_geometry_filler_test.cc b/hoomd/mpcd/test/planar_pore_geometry_filler_test.cc index bb3b9a6aa9..bc027a5e28 100644 --- a/hoomd/mpcd/test/planar_pore_geometry_filler_test.cc +++ b/hoomd/mpcd/test/planar_pore_geometry_filler_test.cc @@ -27,7 +27,7 @@ void planar_pore_fill_basic_test(std::shared_ptr exec_co std::shared_ptr sysdef(new SystemDefinition(snap, exec_conf)); auto pdata = sysdef->getMPCDParticleData(); - auto cl = std::make_shared(sysdef, 2.0, false); + auto cl = std::make_shared(sysdef, make_uint3(10, 10, 10), false); UP_ASSERT_EQUAL(pdata->getNVirtual(), 0); // create slit pore channel with half width 5, half length 8 @@ -125,7 +125,7 @@ void planar_pore_fill_basic_test(std::shared_ptr exec_co * Now, all sides of the U have thickness 0.5. */ pdata->removeVirtualParticles(); - cl->setCellSize(1.0); + cl->setGlobalDim(make_uint3(20, 20, 20)); filler->fill(2); UP_ASSERT_EQUAL(pdata->getNVirtual(), (unsigned int)(4 * 2 * (0.5 * 4.5 + 0.5 * 16 + 0.5 * 4.5) * 20)); @@ -152,7 +152,7 @@ void planar_pore_fill_basic_test(std::shared_ptr exec_co * Test the average fill properties of the virtual particles. */ filler->setDensity(2.0); - cl->setCellSize(2.0); + cl->setGlobalDim(make_uint3(10, 10, 10)); unsigned int N_avg(0); Scalar3 v_avg = make_scalar3(0, 0, 0); Scalar T_avg(0); diff --git a/hoomd/mpcd/test/utils.h b/hoomd/mpcd/test/utils.h index 51ec3e97b0..cf39103485 100644 --- a/hoomd/mpcd/test/utils.h +++ b/hoomd/mpcd/test/utils.h @@ -4,6 +4,7 @@ #ifndef MPCD_TEST_UTILS_H_ #define MPCD_TEST_UTILS_H_ +#include "hoomd/mpcd/CellList.h" #include "hoomd/mpcd/CellThermoCompute.h" namespace hoomd @@ -50,6 +51,29 @@ class AllThermoRequest std::shared_ptr m_thermo; }; +Scalar3 scale(const Scalar3& ref_pos, std::shared_ptr ref_box, std::shared_ptr box) + { + return box->makeCoordinates(ref_box->makeFraction(ref_pos)); + } + +Scalar4 scale(const Scalar4& ref_pos, std::shared_ptr ref_box, std::shared_ptr box) + { + const Scalar3 pos = scale(make_scalar3(ref_pos.x, ref_pos.y, ref_pos.z), ref_box, box); + return make_scalar4(pos.x, pos.y, pos.z, ref_pos.w); + } + +vec3 +scale(const vec3& ref_pos, std::shared_ptr ref_box, std::shared_ptr box) + { + return vec3(scale(vec_to_scalar3(ref_pos), ref_box, box)); + } + +unsigned int make_local_cell(std::shared_ptr cl, int ix, int iy, int iz) + { + const int3 cell = cl->getLocalCell(make_int3(ix, iy, iz)); + return cl->getCellIndexer()(cell.x, cell.y, cell.z); + } + } // end namespace hoomd #endif // MPCD_TEST_UTILS_H_