Procedures

Finalizes object and frees data.

Initialize axis.

Adds a new region to bc_set.

Builds an integer field, where cells=0 denotes interior cells, and cells=1 denotes boundary cells for input variable.

Checks whether there is BC for a given variable on a given region.

Makes sure bounds represent a plane.

Resizes array to accomodate a new element.

Finalizes bc_set and frees memory.

Fetches a pointer to the val array describing the Dirichlet or Neumann BC of a given variable on a given region.

Returns the extents (lo and hi bounds) of a region.

Returns the index of a region, or -1 if not found.

Prints to stdout information on bc_set, for debugging.

Initializes bc_set.

Reads boundary conditions from file.

Sets boundary condition of a given type, for a given variable on a given region.

Updates ghost cells to enforce Dirichlet BC

Updates ghostcells to enforce Neumann BC.

Imposes boundary conditions for a scalar variable.

Updates ghostcells to enforce symmetry BC. Minus version.

Updates ghostcells to enforce symmetry BC. Plus version.

Imposes boundary conditions for a vector field. For symmetry BC, the sign depends is 'plus' or 'minus' depending on the alignment between the vector component and the symmetry direction.

Finds the intersection between block owned by this MPI rank, and the plane defining the region.

Writes bc_set to disk using HDF5. The file structure follows this convention:

Finalizes the block object.

Returns the coordinates of the cell that contains the position p. This subroutine ignores gost cells. As such, it will always return an internal cell of the domain. If the point is located in a ghost cell, the returned cell will be an internal boundary cell that is closest to that ghost cell.

Returns the coordinates of the cell that contains the position p, inclusive of ghost cells.

Prints to stdout information about this block

Initializes block object.

[DEPRECATED] Initializes block object.

Returns block ID and rank of the block where the point is located using a binary search alogirthm. Note that this function assumes that the point is within the domain, i.e., (pmin <= p <= pmax) and that any treatment for periodicity has been previously applied.

Partitions a parent block into sub-blocks based on a given decomposition Nb(3) for parallel simulations. This will also define the partition axes, and update local bounds/extents, and global bounds/extents.

Reads block data using HDF5.

Associate convenience pointers.

Sets block periodicity in each direction.

Defines MPI derived type for communicating ghostcells.

Initializes a uniform grid on this block.

Computes the bounds of the sub-block form the bounds of the parent block. Each sub-block gets about the same number of grid points in each direction.

Updates the dimensional extents of the block.

Updates the ghostcell values of local grid owned by the current MPI rank. Note that each MPI rank stores only its portion of the grid, thus needs to have proper ghostcell values.

Updates mid points.

Updates grid spacing arrays.

Writes block data using HDF5.

Computes Momentum operator RHS for velocity component in x1-direction.

Computes Momentum operator RHS for velocity component in x2-direction.

Computes Momentum operator RHS for velocity component in x3-direction.

Computes bodyforces based on old state.

Perform corrector step: compute pressure at n+1 and divergence-free velocity at n+1.

Performs intermediate IB step>

Performs predictor step: compute intermediate velocity.

Advances Resolved Particle centroids and markers to n+1.

Computes the solid volume fraction (ibVF) by solving a Poisson equation. This subroutine computes the IB normals fields, applies approriate boundary conditions, and takes the divergence, which forms the right-hand side of the poisson equation. It then uses a HYPRE solver to solve this equation. In case where the Poisson operator is singular and using resolved particles, this subroutine will apply a correction that sets the solid volume fraction at particle centroids.

Finalizes solver and frees memory.

Monitors flow data.

Initializes the CDIFS solver.

Links HDF5 Object.

Prepares the boundary conditions used by CDIFS. This subroutine reads pre-existing BCS file on disk. The BCS file must include boundary conditions for restart fields (i.e., V1,V2,V3,P) at minimum. Additional boundary conditions may be required. E.g. if IBs are used, the file must contain boundary conditions for ibVF. In such a case, the subroutine adds additional boundary conditions for ibF, ibN, and ibS based on the specified boundary conditions for ibVF. If no Dirichlet conditions are given for ibVF, it marks the volume fraction Poisson equation as singular.

Prepares block for run. This subroutine reads pre-existing block file on disk and partitions domain based on parameters in the input file.

Prepares bodyorces used by CDIFS.

Prepares fields used by the CDIFS solver. Restart fields (V1,V2,V3,P) are read from file.

Prepares the monitors used by CDIFS.

Prepares operators used by CDIFS. This subroutine also initializes the HYPRE solvers and builds any required operator with the specified boundary conditions.

Generates the divergence operator for the velocity field, and adjusts at the boundaries.

Generates the gradient operator for the pressure field, and adjusts at the boundaries.

Generates the pressure Laplacian operator.

Generates the VF Laplacian operator

Generates the viscous Laplacian operator and adjusts at the boundaries.

Prepares output list used by CDIFS.

Computes collisions between resolved Particles and Immersed Boundaries.

Gets command line options, by looping over command line arguments and finding pairs of the type "-switch value"

Adds an Immersed Boundary to list of collisional objects.

Adds Point Particles to list of collisional objects.

Adds Resolved Particles to list of collisional objects.

Computes collisions between all added objects.

Computes collisions between Point Particles and Immersed Boundaries.

Computes collisions between pairs of Point Particles.

Computes collisions between Point Particles and Walls.

Computes collisions between Resolved Particles and Immersed Boundaries.

Computes collisions between Point and Resolved Particles.

Computes collisions between pairs of Resolved Particles.

Computes collisions between Resolved Particles and Walls.

Finalizes object and frees memory.

Initializes object.

Prepares object for use in solvers.

Frees data: removes ghost objects and frees neighbor lists.

Initializes cblock to handle collisions. This extra block is expected to be coarser than the simulation block, but larger than the maximum object size. It is used to expedite neighbor searches.

Initializes cblock to handle collisions. This extra block is expected to be coarser than the simulation block, but larger than the maximum object size. It is used to expedite neighbor searches.

Updates ghost objects in preparation for collisions.

Updates neighbor lists in preparation for collisions.

Returns the cross product of two vectors.

Returns the cross product of two vectors.

Returns the cross product of two vectors.

Computes collisions with a Linearized Spring Dashpot model.

Wrapper function for "cudaDeviceGetAttribute"

Wrapper function for "cudaGetDeviceCount"

Get information about GPU

Wrapper function for "cudaMallocManaged"

Performs addition of integer Eulerian objects.

Performs addition of real Eulerian objects.

Updates and add-up the ghostcells.

Adds up ghostcells in the x direction with non-blocking mpi directives.

Adds up ghostcells in the y direction with non-blocking mpi directives.

Adds up ghostcells in the z direction with non-blocking mpi directives.

Allocates Cell array in Eulerian object.

Performs assignment for Eulerian_obj.

Performs assignment for Eulerian_obj.

Performs assignment for Eulerian_obj.

Deallocate Cell array in Eulerian object.

Finalizes the Eulerian object and free memory.

Prints info about this structure.

Initializes an Eulerian field.

Computes the mean of an Eulerian_obj.

Performs multiplication of integer Eulerian objects by integer scalar.

Performs multiplication of real Eulerian objects by real scalar.

Computes norm2 of an Eulerian_obj.

Performs subtraction of integer Eulerian objects.

Performs subtraction of real Eulerian objects.

Updates the ghostcells.

Updates the ghostcells in the x direction with non-blocking mpi directives.

Updates the ghostcells in the y direction with non-blocking mpi directives.

Updates the ghostcells in the z direction with non-blocking mpi directives.

Adds a eulerian object to the eulerian set.

Finalizes object and frees up memory.

Returns the index of an Eulerian_obj contained in this%fields given its name.

Returns whether overwriting is true or false

Returns the base name of file to write

Returns the base name of file to write.

Prints info about this collection of eulerian objects

Initializes an Eulerian Set.

Reads Eulerian data using H5HUT.

Reads Eulerian data with LEAP's HDF5.

Reads one Eulerian object based on name with H5HUT.

Reads one Eulerian object based on name using LEAP's HDF5.

Sets file overwritting

Set the base name of file to read

Sets the base name of file to write.

Writes Eulerian data using H5HUT.

Write Eulerian data using LEAP's HDF5.

Write Eulerian data using SILO.

Write a single Eulerian object to file using H5HUT.

Write a single Eulerian object to file using LEAP's HDF5.

Write a single Eulerian objects to file using SILO.

Compute collision forces

Computes the solid volume fraction (ibVF) by solving a Poisson equation. This subroutine computes the IB normals fields, applies approriate boundary conditions, and takes the divergence, which forms the right-hand side of the poisson equation. It then uses a HYPRE solver to solve this equation. In case where the Poisson operator is singular and using resolved particles, this subroutine will apply a correction that sets the solid volume fraction at particle centroids.

Finalizes solver and frees memory.

Initializes the GRANS solver.

Links HDF5 Object.

Prepares the boundary conditions used by GRANS. Note that the only boundary conditions required by GRANS are those in connection with the volume fraction Poisson equations. This subroutine reads pre-existing BCS file on disk. It adds additional boundary conditions for ibF, ibN, and ibS based on the specified boundary conditions for ibVF. If no Dirichlet conditions are given for ibVF, it marks the volume fraction Poisson equation as singular.

Prepares block for run. This subroutine reads pre-existing block file on disk and partitions domain based on parameters in the input file.

Prepares the collision utility used by GRANS. If the collision grid spacing is not provided, this subroutine makes it equal to the largest particle diameter. Collisions with IBs are default to true, but can be turned off. Users can use collisions with walls instead (for simple geometries). Additional parameters are read in the Prepare subroutine of the collision object.

Prepares fields used by the GRANS solver.

Prepares the monitors used by GRANS.

Prepares operators used by GRANS. This subroutine also builds the volume fraction Poisson operator with the specified boundary conditions.

Prepares output list used by GRANS.

Finalizes object and frees memeory.

Gets number of fields in step.

Gets number of data points in step. H5HUT assumes that all datasets have the same number of points, thus we return the number of points of the first dataset we find.

Counts and returns number of steps in file.

Initializes structure.

Jumps to a specific step.

Gets information about the last step.

Creates a new step and updates attributes.

Reads Lagrangian/1D data fom a h5hut file. If no offset is provided, uses default h5hut file view. Otherwise, sets file view manually.

Reads Eulerian/3D data from a h5hut file.

Reads scalar attributes.

Reads an array of attributes.

Sets the current step in file, and possibly create a new one, if this step does not exist yet.

Returns number of steps.

Writes Lagrangian/1D data to a h5hut file.

Writes Eulerian/3D data to a h5hut file.

Writes scalar attributes.

Writes an array of attributes.

Writes grid attributes.

Initializes the hashtable.

Closes hdf5 file.

Closes an HDF5 group and removes it from the hashtable.

Creates a group (analogous to directory) in an HDF5 file and updates hash table.

Finalizes object and frees memory.

Function that will append and prepend '/' if missing.

Returns the HDF5 object id of the group.

Returns the number of points in a dataset given by name under group given by name.

Initializes the hdf5 object.

Opens a hdf5 file given by name with mode stated by flag. This can take one of these values: 'R' for read only 'W' for write only (will delete existing file) 'RW' for read-write

Opens a group (analogous to directory) in an HDF5 file and updates hash table.

Reads a 1D dataset located under groupname and given by name. If no offset is provided, uses default file view. Otherwise, sets file view manually.

Reads a 3D dataset located under groupname and given by name.

Read a scalar attribute under a given group.

Read a 1-D array of attributes under a given group.

Reads coordinates from HDF5 file. Only the root MPI rank does the reading, and then broadcasts to other MPI ranks.

Reads the dataset names under a given base group in an HDF5 file.

Reads the groups (i.e., directories) under a given base group in an HDF5 file.

Writes an array/1D data to a HDF5 file.

Writes Eulerian/3D data to a HDF5 file.

Writes a scalar attribute.

Writes an array of attributes.

Writes coordinates to HDF5 file. Only the root MPI rank does the writing.

Sets the coefficients of the matrix.

Define the entries of the matrix Ax=b one row at a time Finite difference/Finite volume 2nd order Laplacian: ddu/dxdx = -2 u(i,j,k)/dxdx + u(i-1,j,k)/dxdx + u(i+1,j,k)/dxdx ddu/dydy = -2 u(i,j,k)/dydy + u(i,j-1,k)/dydy + u(i,j+1,k)/dydy ddu/dzdz = -2 u(i,j,k)/dzdz + u(i,j,k-1)/dzdz + u(i,j,k+1)/dzdz

Destroys objects/pointers and clears data.

Initializes the hypre object.

Prints the matrix coefficients for debugging.

Selects one of the preconfigured solvers and get solver-specific parameters.

Sets the entries of the rhs vector, one element at a time.

Sets the entries of the rhs vector, one element at a time.

Set the entries of the rhs vector for the Struct interface.

Sets up the hypre objects in preparation for solves. Note: Setting up HYPRE is an expensive operation so it's best to do this only once during a simulation as opposed to setting-up and destorying each time-step.

Sets up the hypre grid.

Sets up matrix with IJ interface.

Sets up and builds the matrix.

Sets up pointers for IJ solver.

Sets up the rhs vector.

Sets up the rhs vector.

Sets up row indexing used with IJ interface.

Setup the solution vector, and initialize it to zero

Sets up solver with IJ interface.

Setup the solution vector, and initialize it to zero

Sets up the hypre solver.

Sets up the discretization stencil. Each entry represents the relative offset (in index space) E.g.: a 2D 5-pt stencil would have the following geometry -- Offset { {0,0}, {-1,0}, {1,0}, {0,-1}, {0,1} } E.g.: a 3D 7-pt stencil would have the following geometry -- Offset { {0,0,0}, {-1,0,0}, {1,0,0}, {0,-1,0}, {0,1,0}, {0,0,-1}, {0,0,1} }

Solves the system Ax=b and return the solution.

Solves the system Ax=b and return the solution, IJ interface.

Solves the system Ax=b and return the solution, Struct interface.

Integral of box filter from 0 to r.

Integral of cosine filter from 0 to r.

Integral of second cosine filter from 0 to r.

Integral of parabolic filter from 0 to r

Integral of Roma and Peskin's filter from 0 to r.

Integral of triangle filter from 0 to r.

Integral of triweight filter from 0 to r.

Gets a bump function centered on the lagrangian object.

Interpolates a field f defined on an Eulerian stencil to the location of a lagrangian object

Locates a Lagrangian object on an external grid. Returns the location of the cell containing the object.

Applies periodic boundary conditions.

Communicates lagrangian objects across MPI_rank. This subroutine relies on a rank locator procedure (GetOwnerRankOpt) to determine the rank that should own each Lagrangian object. The default rank locator is the one provided by the block object associated with this Lagrangian_set. From there, each rank will send objects that they no longer own and receive objects from other ranks that belongs to it. Note that this subroutine allocates an array (buf_send) of size (MAX NUMBER of OBJECTS to SEND) x (NUMBER OF MPI RANKS) For massively parallel simulations, this may cause out of memory issues. In those cases, care must be exercised to reduce the number of objects to be sent at any given time (e.g.: by doing communications in small batches).

Creates an MPI data type for parallel communication of the Lagrangian objects.

Finalizes the structure and frees memory.

Frees the MPI data type.

Returns whether overwriting is true or false.

Returns the MPI rank that should own this lagrangian object based on which block it belongs to.

Returns the base name of file to read.

Returns the base name of file to write.

Prints diagnostics information about the derived type to the standard output.

Initialize lagrangian objects related IO.

Localizes all Lagrangian object on the grid. For each Lagrangian object in the set, this subroutine finds the cell (staggering=0) where this object is located and updates its cell indices.

Sorting routine: stacks active lagrangian objects (i.e., who's id is >=1) at the beginning of the array then resizes. Objects with id <= 0 (such as ghost objects) are removed by this subroutine.

Changes the size of an array of Lagrangian objects. To avoid excessive reallocating, the object array will be reallocated only if the new size is (1+RESIZE_INCREMENT) larger or (1-RESIZE_INCREMENT) smaller than previous size. When the size change does not justify reallocating, the excess objects at the end tail of the object array will be marked as inactive with a large negative ID.

Sets the interpolation and extrapolation filter kernels. Default is the Triangle kernel.

Adjusts the filter half size. Note that the block needs to contain enough ghost cells to be able to represent a filter kernel centered on the edge of the domain. Otherwise, an error will be returnned. The larger the filter size, the more ghost cells are required.

Sets file overwritting.

Sets the base name of file to read.

Sets the base name of file to write.

Updates the total count of Lagrangian objects.

Updates ghost objects. Copies objects that lie "dist"-away from the block's boundaries to neighboring MPI-ranks and designate copies as Ghost Objects (id<0). This subroutine will also update the local count (i.e., this%count_) to (NBR of ACTIVE OBJECTS) + (NBR of GHOST OBJECTS). However, the global count (this%count) will remain unchanged (i.e., equal to the total count of active ojbects only)0

Updates ghost objects in the idir direction. Copies objects that lie "dist"-away from the block's boundaries in idir-direction to neighboring MPI-ranks. Copied objects get a negative ID to designate them as ghost objects

Assignment

Adds an IB cylinder (with open faces).

Adds an IB plane.

Adds an IB sphere.

Finds the center of area.

Computes the solid volume fraction on the mesh.

Computes a filtered quantity on the Eulerian grid.

Finalizes the marker_set type. This subourtine replaces the inheritted lagrangian_final.

Computes the IB forcing Interpolation are carried out by trilinear interpolations.

Initializes the marker_set type. This subourtine replaces the inheritted lagrangian_init.

Loads markers from a binary STL. This is a serial routine.

Prepares marker_set for use with solvers.

Reads marker data from file in parallel using H5HUT.

Reads marker data from file in parallel using HDF5.

Sets up parameters for creating the MPI derived type. Create the MPI structure

Sets the sample type used in allocation of polymorphic variables.

Sets the chunk size.

Updates the Normals field.

Updates the Surface Density Function.

Writes marker data to file in parallel using H5HUT.

Write marker data to file in parallel using HDF5.

Finalizes the object and frees memory.

Defines how to print values. Format specifier for an integer Format specifier for a real Format specifier for a logical Format specifier for a full line

Intializes a single monitor.

Prints to file or stdout content of the monitor

Sets the value in the nth column of a monitor.

Creates a new monitor.

Changes the size of monitors arrays to add 1 element.

Finalizes object and frees memory.

Returns the ID of a monitor identified by name.

Print a number of diagnostics information.

Initializes a set of monitors.

Prints content of monitors.

Sets the label or value of a column ofa a monitor given by name.

Applies Dirichlet boundary conditions to the RHS of a Laplacian equation.

Builds Laplacian operator using Morinishi's schemes.

Computes d(U1 U1)/dx1.

Computes d(U1 U2)/dx1.

Computes d(U1 U1)/dx1.

Computes d(U2 U1)/dx2.

Computes d(U2 U2)/dx2.

Computes d(U2 U1)/dx2.

Computes d(U3 U1)/dx1.

Computes d(U3 U1)/dx1.

Computes d(U3 U1)/dx1.

Computes the derivative in the x1-direction. Note: If input is face-centered (on x1), result is cell-centered (on x1m). If input is cell-centered (on x1m), result is face-centered (on x1).

Computes the derivative in the x2-direction. Note: If input is face-centered (on x2), result is cell-centered (on x2m). If input is cell-centered (on x2m), result is face-centered (on x2).

Computes the derivative in the x3-direction. Note: If input is face-centered (on x3), result is cell-centered (on x3m). If input is cell-centered (on x3m), result is face-centered (on x3).

Computes the divergence of a vector (in1,in2,in3). This function takes in1,in2,in3 cell-centered (stag=0) and returns the divergence on cell centers (stag=0)

Finalizes object and frees memory.

Initializes object. The operator order can be specified by the optional parameter. Otherwise, the object initializes 2nd order operators by default.

Interpolates in the x1-direction. Note: If input is face-centered (on x1), result is cell-centered (on x1m). If input is cell-centered (on x1m), result is face-centered (on x1).

Interpolates in the x2-direction. Note: If input is face-centered (on x2), result is cell-centered (on x2m). If input is cell-centered (on x2m), result is face-centered (on x2).

Interpolates in the x3-direction. Note: If input is face-centered (on x3), result is cell-centered (on x3m). If input is cell-centered (on x3m), result is face-centered (on x3).

Computes the strain rate tensor from the velocity field. Result is on mid points (staggering=0). Tensor is stored as follows: S = 0.5*( grad(u) + grad(u)^T ) ( S(1) S(4) S(6) ) = ( S(4) S(2) S(5) ) ( S(6) S(5) S(3) )

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

MPI Broadcast operation from root rank.

Finalizes MPI and the parallel environment.

Initializes the parallel environement.

MPI LOGICAL OR reduction operation.

MPI LOGICAL OR reduction operation.

MPI MAX reduction operation.

MPI MAX reduction operation.

MPI MAX reduction operation.

MPI MAX reduction operation.

MPI MIN reduction operation.

MPI MIN reduction operation.

MPI MIN reduction operation.

Determines if this rank is the root rank.

Subroutine to gracefully stop the execution with an optional error message.

MPI SUM reduction operation.

MPI SUM reduction operation.

MPI SUM reduction operation.

MPI SUM reduction operation.

MPI SUM reduction operation.

MPI SUM reduction operation.

MPI SUM reduction operation.

MPI SUM reduction operation.

Returns the elapsed time since an arbitrary origin. Note that different ranks return different WTIMEs.

Builds a Cartesian topolgy with MPI. Define a root processor at coordinates (1,1,1)

Resizes entries array to add a new entry.

Sets 0D (scalar) value equal to 0D (scalar) default.

Sets 1D (array) values equal to 1D (array) defaults.

Returns ID of label in entries array. Returns 0 if label not found.

Finalizes object and frees allocated memory.

Initializes the parser object.

Checks whether a label was found when parsing the file.

Parses an ASCII file. This subroutine will identify all entries in the file (label-value pairs) and store them internally. Users can specify the filename using the optional optInput variable. Otherwise, the default filename is 'input'.

Parses a line by finding the label-value pair and storing it as a new entry.

Prints all variables found in the parsed file.

Reads 0D (scalar) values of kind real, integer, logical, or character string. If label is not found and the optional default is provided, the value will be set to the default value. If the label is not found and there is no optional default, this subroutine will return an error.

Reads 1D (array) values of kind real, integer, logical, or character string. If label is not found and the optional default is provided, the value will be set to the default value. If the label is not found and there is no optional default, this subroutine will return an error.

Fomats a line by removing comments and replacing tabs with spaces.

Assignment

Assignment

Advances centers to next timestep.

Changes Particle Type. This deletes all existing particle data and redeclares the associated MPI type.

Creates monitor file for Point Particles.

Filters a quantity to the Eulerian grid.

Prepares for use with solvers.

Reads particle data from file in parallel using H5HUT.

Reads particle data from file in parallel using HDF5.

Sets up parameters used when creating the MPI derived type.

Sets up parameters used when creating the MPI derived type of particles with BH type.

Sets up parameters used when creating the MPI derived type of particles with default type.

Sets the sample type used in allocation of polymorphic variables.

Stores values from previous timestep.

Updates monitoring data.

Writes particle data to file in parallel using H5HUT.

Writes particle data to file in parallel using HDF5.

Writes particle data to file in parallel using SILO.

Adds a new variable to region.

Resizes array to accomodate a new element.

Returns index of a variable in this region, or -1 if not found.

Initializes a region

Assignment

Advances centers to next timestep

Advances markers to next timestep

Creates monitor file for Resolved Particles

Filters a quantity to the Eulerian grid

Finalizes the ResPart_set type. This subourtine replaces the inheritted lagrangian_final.

Computes average solid volume fraction at particle centroids

Computes hydrodynamic force on particle.

Computes the IB forcing

Returns the MPI rank of the lagrangian centroid owning this marker.

Computes hydrodynamic stresses on markers

Initializes the ResPart_set type. This subourtine replaces the inheritted lagrangian_init.

Prepares ResPart_set for use with solvers.

Reads ResPart data from file using H5HUT.

Reads ResPart data from file with HDF5.

Regroup markers with their respective centroids on the same MPI block

Filters a quantity to the Eulerian grid

Sets up parameters used when creating the MPI derived type.

Sets the sample type used in allocation of polymorphic variables.

Sets the base name of file to read.

Sets the base name of file to write.

Stores values from previous timestep

Update lookup array -- The lookup array returns the local (MPI rank) index of a centroid when given the global ID of that centroid

Updates the Normals field

Updates the Surface Density Function

Writes ResPart data to file using H5HUT.

Writes ResPart data to file using HDF5.

Writes data to disk in Silo format.

Sets up silo groups for poor man's IO. Splits MPI ranks into groups of size nproc_node. Each group writes squentially to its own file.

Finalizes structure and frees memory.

Initialize structure.

Creates a new Silo virtual data base (VDB) for this timestep.

Creates silo files and their internal structure.

Writes grid attributes.

Writes Lagrangian mesh attributes.

Writes 1D array to a hdf5 file with silo.

Writes Eulerian/3D data to a hdf5 file with silo.

Free all data associated with this list.

Traverse the list until key is found. Returns the associated value to the key, or -1 if key not found.

Traverse the list until key is found. Returns the associated value to the key, or -1 if key not found.

Traverse the list until key is found. Returns the associated value to the key, or -1 if key not found.

Traverse the list until key is found. Returns the associated value to the key, or -1 if key not found.

Adds a pair key-value to the list.

Remove key-value pair from list.

Communicates markers of all solids in this set.

Filters a quantity to the Eulerian grid.

Finalizes object and frees memory.

Initializes a collection of solids.

Localizes markers of all solids in this set on the grid.

Reads all solids from disk using H5HUT.

Reads all solids from disk using HDF5.

Selects interpolation and extrapolation kernels.

Changes filter size to desired value.

Sets file overwritting

Sets the names of files to read.

Sets the names of files to write.

Writes all solids to disk using H5HUT.

Writes all solids to disk using HDF5. Add some attributes

Removes file extension from filename while preserving scientific notation and dots in paths.

Removes path from filename.

Creates a directory using system commands.

Deletes a directory using system commands.

Deletes a file.

Checks whether a file exists.

Adds timing info.

Determines whether simulation is over.

Changes run status to finished.

Finalizes and frees memomry.

Returns timing information for data given by name.

Initializes the timer.

Moves timer from n to n+1

Determine whether it is time to write visualization files.

Determine whether it is time to write restart files.

Updates timing info with elapsed time since beginning of current iteration.

Frees up data stored by this XDMF attribute.

Frees up data stored by this XDMF grid.

Adds field information to the xdmf object.

Adds grid information to the xdmf object.

Finalizes object and frees memmory.

Initialize XDMF object.

Resizes the fields array in an xdmf object. Note that resizing occurs in increaments of size (RESIZE_INCREMENT). By default, RESIZE_INCREMENT=10, meaning that if resizing occurs, it will increase or reduce the array size by 10 slots. This is done to avoid frequent reallocating.

Write the XDMF info to a file. This is a serial subroutine and should be called by only one rank.