Procedures

Incremental running-mean update: $\bar{x}_n = \bar{x}_{n-1} + (x_n - \bar{x}_{n-1})/n$ where stat_inc = 1/n.

Compute derived fields from the velocity gradient tensor.

Interpolates the pressure field from CELL (DIR_Z) to VERT (DIR_X) for snapshot output and rescales from pseudo-pressure to physical (kinematic) pressure.

From the global rank maps, fills in the rank position as well as the previous and next rank in the par structure

Copies cell_dims information to vert_dims taking periodicity into account

Copies vert_dims information to cell_dims taking periodicity into account

Allocate memory for a new block and return a pointer to a new m_allocator object.

Constructor function for the cuda_tdsops_t class. See tdsops_t for details.

Wrapper for curl

Curl of a vector field (u, v, w).

Performs 2D mesh decomposition using 2decomp&fft

Full (forward + backward) non-periodic pentadiagonal Thomas solve on CPU. Mirrors the CUDA der_penta_full kernel; operates on 2D (SZ, n) arrays.

Full (forward + backward) non-periodic pentadiagonal Thomas solve.

Cyclic pentadiagonal compact solve via Sherman-Morrison-Woodbury rank-4 correction. A_cyc = A_np + U*W^T where U = [e_1,e_2,e_{n-1},e_n] and W^T encodes the four corner coupling pairs; A_np is the non-periodic Thomas factorisation in (ffr,...).

Periodic pentadiagonal Thomas solve via Sherman-Morrison-Woodbury rank-4.

Go through the block list from head to tail, deallocating each memory block in turn. Deallocation of a m_allocator object automatically deallocates its internal allocatable data array.

Divergence of a vector field (u, v, w).

Wrapper for divergence_v2p

Combined X and Y periodicity enforcement (interleave shuffle).

Single-GPU non-periodic pentadiagonal compact-FD solve.

Single-pass non-periodic pentadiagonal compact-FD solve on CPU. No MPI exchange is needed; each group is solved independently.

Cyclic pentadiagonal compact-FD solve via Sherman-Morrison-Woodbury. Halos u_recv_s/e must be set to periodic-extension values by the caller.

Cyclic pentadiagonal compact-FD solve via Sherman-Morrison-Woodbury. Halos u_recv_s/e must be set to periodic-extension values by the caller.

Backward FFT for 110 case: C2R then transpose (nz,nx,ny)->(nx,ny,nz)

Forward FFT for non-periodic-X case We transpose X<->Y so that the non-periodic direction becomes the "Y" direction in the transposed space, then use the same FFT approach as 010

Forward FFT for 110 case: transpose (nx,ny,nz)->(nz,nx,ny) then R2C

if stretching in y is 'bottom'

Spectral post-processing for 110 case (R2C Z-transpose) 7 separate kernel launches to avoid cross-block race conditions. Spectral array is (nz/2+1, nx, ny) = (nx_spec, ny_spec, nz_spec). Thread i->X (ny_spec), blockIdx%y k->Y (nz_spec), serial j->Z (nx_spec).

m_base_backend

m_base_backend

m_base_backend

Set domain X_FACE boundary values. c_start: Dirichlet value applied at the left face (i = 1) c_end: convective velocity Uc = uxmax * gdt / dx, used as multiplier in the outflow scheme du/dt + Uc*du/dx = 0

Set domain Y_FACE boundary values. c_start: Dirichlet value applied at the bottom face (j = 1) c_end: Dirichlet value applied at the top face (j = ny)

volume integral of a field

volume integral of a field

Return a pointer to the first available memory block, i.e. the current head of the block list. If the list is empty, allocate a new block with create_block first.

Utility function that returns a array made of the id of the block currently in the block list. Return the array [0] if block list is empty.

Get the coordinates of a vertex with i, j, k local cartesian indices Avoid calling this in hot loops

Getter for local domain dimensions

Getter for domain dimensions

Extract data from field f optionally reordering into dir orientation. To output in same orientation as f, use call ...%get_field_data(data, f, f%dir)

Getter for local domain dimensions

Get application storage directional index from cartesian index

Get cartesian index from application storage directional one

Converts indices in between any two DIR_?

Getter for the main dimension a field oriented along dir with data on data_loc

Getter for the main dimension of field phi

Returns RDR_?2? value based on two direction inputs

Gradient of a scalar field 'p'.

Wrapper for gradient_p2v

Check whether a field name is present in the output_fields list.

Interpolation of a scalar field from cell centres to vertices.

Returns wether or not the current rank is the root rank

Laplacian of a scalar field 'u'.

Copy data between x3d2 padded arrays and cuFFTMp descriptors

Copy with transpose: src(nx, ny, nz) -> dst(ny, nx, nz) Used for 100 case forward FFT

Copy with transpose back: src(ny, nx, nz) -> dst(nx, ny, nz) Used for 100 case backward FFT

Completely initialise the mesh object. Upon initialisation the mesh object can be read-only and shouldn't be edited Takes as argument global information about the mesh like its length, number of cells and decomposition in each direction

Obtains global coordinates for all the vertices and midpoints

LU preprocessing for non-periodic pentadiagonal Thomas algorithm.

Reports the div(u) at cell centres

Reports the enstrophy

Post-processes the divergence of velocity in spectral space, including scaling w.r.t. grid size.

Post-process div U* in spectral space for all periodic BCs.

Post-processes the divergence of velocity in spectral space, including scaling w.r.t. grid size.

Post-process div U* in spectral space, for non-periodic BC in y-dir.

Post-processes the divergence of velocity in spectral space, including scaling w.r.t. grid size.

Post-processes the divergence of velocity in spectral space, including scaling w.r.t. grid size.

Solve the Poisson equation at cell centres with non-perioic BC along y

Step 1 (forward): normalise + Z periodic post-process Z is dim1 (serial j loop), periodic R2C — no sign flip needed since j only goes to nz/2+1.

Step 4: Poisson solve — divide by waves

Step 6 (backward): X paired even/odd recombine

Step 2 (forward): X paired even/odd split X is dim2 (thread i). Only i in [2, nx/2+1] executes. Writes to i and nx-i+2. Race-free (pair doesn't enter).

Step 5 (backward): Y paired even/odd recombine

Step 3 (forward): Y paired even/odd split Y is dim3 (blockIdx%y = k). Only k in [2, ny/2+1] executes. Writes to k and ny-k+2. Race-free (pair block doesn't enter).

Step 7 (backward): Z periodic undo

Release memory block pointed to by HANDLE to the block list. It is pushed to the front of the block list, in other words it is made the head block.

Runs the solver forwards in time from t=t_0 to t=T, performing postprocessing/IO and reporting diagnostics.

m_base_backend

m_base_backend

m_base_backend

Reduces a single slice f(i_slice, :, :) (in the kernel's packed-pencil indexing). Signed max/sum, no abs. One thread per (y, z) point.

m_base_backend

Stretching necessitates a special operation in spectral space. The coefficients for the operation are stored in matrix form.

Constructor function for the tdsops_t class.

Thomas algorithm implementation. So much more easier than the distributed algorithm. It is intended to work only on a single rank so there is no MPI communication.

Skew-symmetric form of convection-diffusion terms in the incompressible Navier-Stokes momemtum equations, excluding pressure terms. Inputs from velocity grid and outputs to velocity grid.

low memory version of the transport equation, roughly %2 slower overall

Skew-symmetric form of convection-diffusion terms in the species equation. Inputs from velocity grid and outputs to velocity grid.

Compute the convection and diffusion for the given field in the given direction. Halo exchange for the given field is necessary When sync is true, halo exchange of momentum is necessary

Compute the convection and diffusion for the given field in the given direction. Halo exchange for the given field is necessary When sync is true, halo exchange of momentum is necessary

Used before R2C FFT for 110 case to put Z (periodic) in fast dim.

Transpose back: src(nz, nx, ny) -> dst(nx, ny, nz) Used after C2R FFT for 110 case.

Combined X and Y periodicity undo (reverse interleave shuffle).

m_base_backend

m_base_backend

Spectral equivalence constants