diff --git a/.buildinfo b/.buildinfo new file mode 100644 index 00000000..21507e76 --- /dev/null +++ b/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 55bbeec6713c446da927a8d32b6a92d3 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/Debugging.html b/Debugging.html new file mode 100644 index 00000000..5ad1f8a8 --- /dev/null +++ b/Debugging.html @@ -0,0 +1,164 @@ + + + + + + + Debugging — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Debugging

+

Debugging is an art. Everyone has their own favorite method. Here we +offer a few tips we have found to be useful.

+

Compiling in debug mode (e.g., make DEBUG=TRUE for gmake users; +cmake -DDEBUG for cmake users) and running with +amrex.fpe_trap_invalid=1 in the inputs file can be helpful. +In debug mode, many compiler debugging flags are turned on and all +MultiFab s are initialized to signaling NaNs. The +amrex.fpe_trap_invalid parameter will result in backtrace files +when a floating point exception occurs. One can then examine those +files to track down the origin of the issue.

+

Several ways to look at the data include:

+
    +

  1. Writing a MultiFab to disk with

    +
    VisMF::Write(const FabArray<FArrayBox>& mf, const std::string& name);
+
    +
    +

    and examining it with Amrvis (section Amrvis in the AMReX documentation).

    +
    2. +

  2. You can also use the print_state routine:

    +
    void print_state(const MultiFab& mf, const IntVect& cell, const int n=-1);
+
    +
    +

    which outputs the data for a single cell.

    +
    3. +

  3. If you want to compare old and new plotfiles,

    +
    fcompare --infile1 plt00000_run1 --infile2 plt00000_run2 --diffvar u_g
+
    +
    +

    will print out the maximum absolute and relative differences between the two plotfiles +for each variable and will also create a new plotfile “diffs” that contains the difference +in u_g (in this case) between the two plotfiles.

    +

    The fcompare executable can be built in AMReX (go to amrex/Tools/Plotfile and type “make”).

    +
    4. +
+

Valgrind is another useful debugging tool. Note that for runs using +more than one MPI process, one can tell valgrind to output to different +files for different processes. For example,

+
+
mpiexec -n 4 valgrind --leak-check=yes --track-origins=yes --log-file=vallog.%p ./incflo.exe ...
+
+
+
+

Also see AMReX’s documentation on Debugging for further suggestions.

+

If you believe you’ve encountered a bug or incorrect behavior in incflo, please report the issue +on incflo’s github page here .

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/EB.html b/EB.html new file mode 100644 index 00000000..67dccfa0 --- /dev/null +++ b/EB.html @@ -0,0 +1,140 @@ + + + + + + + Embedded Boundaries — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Embedded Boundaries

+

incflo follows AMReX’s approach to embedded boundaries (EB), which is described in the +AMReX EB documentation. +By default, incflo uses AMReX’s constructive solid geometry framework defined in the namespace amrex::EB2. +Alternatively, the constructive solid geometry can also be created using OpenSCAD’s CSG file format by installing +the csg-eb library. To use this option, incflo must be built with the flag +USE_CSG=TRUE and CSGEB_HOME must be set to where the library was installed. +See MFIX’s CSG-EB repository for more details about this format.

+

incflo provides several options of embedded boundary geometries. The inputs parameter incflo.geometry = XXX +determines which geometry is selected by incflo::MakeEBGeometry() within incflo/src/embedded_boundaries. +The procedure to create your own EB geometry is described in the AMReX documentation on Initializing the Geometric Database. +As discussed in the AMReX documentation, note that when constructing the EB, we must specify a +maxium coarsening level (max_crse_level):

+
EB2::Build(gshop, geom[lev], required_crse_lev, max_crse_level);
+
+
+

This specifies to which level of coarseness the EB is still defined. It might not be +immediately obvious, but the multigrid solver (used in the fluid solve) also +depends indirectly on this parameters. Choosing a value of max_crse_level that is too small might restrict +how many levels the MLMG solver can use, and therefore give slightly different answers in the fluid solve.

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/FluidEquations.html b/FluidEquations.html new file mode 100644 index 00000000..64cc489a --- /dev/null +++ b/FluidEquations.html @@ -0,0 +1,178 @@ + + + + + + + Fluid Variables — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Fluid Variables

+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Variable

Definition

\(\rho\)

Fluid density

\(U\)

Fluid velocity

\(\tau\)

Viscous stress tensor

\(\mu_s\)

scalar diffusivity

\({\bf g}\)

Gravitational acceleration

\({\bf H}_U\)

\(= (H_x , H_y , H_z )\), External Forces

\(H_s\)

External sources

+
+
+
+

Fluid Equations

+

Conservation of fluid mass:

+
+\[\frac{\partial \rho}{\partial t} + \nabla \cdot (\rho U) = 0\]
+

Conservation of fluid momentum:

+
+\[\frac{ \partial (\rho U)}{\partial t} ++ \nabla \cdot (\rho U U) + \nabla p = \nabla \cdot \tau + {\bf H}_U\]
+

Incompressibility constraint:

+
+\[\nabla \cdot U = 0\]
+

Tracer(s):

+
+\[\frac{\partial \rho s}{\partial t} + \nabla \cdot (\rho U s) = \nabla \cdot \mu_s \nabla s + \rho H_s\]
+

By default, \(H_s = 0\) and \({\bf H}_U = {\bf 0}\). +If gravity is set during runtime, then \({\bf H}_U\) defaults to \(\rho {\bf g}\)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Fluids_Chapter.html b/Fluids_Chapter.html new file mode 100644 index 00000000..3dffc879 --- /dev/null +++ b/Fluids_Chapter.html @@ -0,0 +1,139 @@ + + + + + + + Solving the Fluid Equations — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +

Here we describe the fluid variables, the governing equations, and the time discretization +of the fluid evolution.

+
+

Solving the Fluid Equations

+
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/GettingStarted.html b/GettingStarted.html new file mode 100644 index 00000000..98c2ffbb --- /dev/null +++ b/GettingStarted.html @@ -0,0 +1,480 @@ + + + + + + + Getting Started — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Getting Started

+

This section walks you through a brief introduction to using incflo.

+
+

Downloading the code

+

incflo is built on top of the AMReX framework. In order to run +incflo, you must download separate git modules for incflo, AMReX +and AMReX-Hydro.

+

First, make sure that git is installed on your machine.

+
    +

  1. Download the AMReX repository by typing:

    +
    git clone https://github.com/AMReX-Codes/amrex.git
+
    +
    +

    This will create a folder called amrex/ on your machine. +For additional information on downloading the AMReX source code see AMReX user guide - Downloading the code.

    +
    2. +

  2. Download the AMReX-Hydro repository by typing:

    +
    git clone https://github.com/AMReX-Fluids/AMReX-Hydro.git
+
    +
    +

    This will create a folder called AMReX-Hydro/ on your machine.

    +
    3. +

  3. Download the incflo repository by typing:

    +
    git clone https://github.com/AMReX-Fluids/incflo.git
+
    +
    +

    This will create a folder called incflo/ on your machine.

    +
    4. +
+

You will want to periodically update each of these repositories +by typing git pull within each repository.

+

Next, you can choose to either Building with GNU Make or Building with CMake.

+
+
+

Building with GNU Make

+

Here, we walk you through compiling an incflo executable. +Decide whether you want to build the executable in 2-D vs 3-D, +with or without EB (embedded boundaries / cut cells), and choose the corresponding +directory: test_2d, test_3d, test_no_eb_2d, or test_no_eb. +For this example, let’s say you want to build in 2-D with cut cells. +Then to build the code:

+
    +

  1. cd to the desired build directory; e.g.

    +
    cd incflo/test_2d
+
    +
    +
    2. +

  2. Edit the GNUmakefile:

    +

    Set AMREX_HOME to be the path to the directory where you have put amrex. NOTE: when setting AMREX_HOME in the GNUmakefile, be aware that ~ does not expand, so AMREX_HOME=~/amrex/ will yield an error.

    +

    Alternatively, the path to AMReX can be set up as an environment variable, AMREX_HOME, on your machine to point to the path name where you have put AMReX. For example, if you are using the bash shell, you can add this to your .bashrc as:

    +
    export AMREX_HOME=/path/to/amrex
+
    +
    +

    alternatively, in tcsh one can set

    +
    setenv AMREX_HOME /path/to/amrex
+
    +
    +

    Common options that you can set in the GNUMakefile include

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    Option name

    Description

    Possible values

    Default +value

    COMP

    Compiler (gnu or intel)

    gnu / intel

    None

    USE_MPI

    Whether to enable MPI

    TRUE / FALSE

    FALSE

    USE_OMP

    Whether to enable OpenMP

    TRUE / FALSE

    FALSE

    USE_CUDA

    Whether to enable CUDA

    TRUE / FALSE

    FALSE

    DEBUG

    Whether to use DEBUG mode

    TRUE / FALSE

    FALSE

    PROFILE

    Include profiling info

    TRUE / FALSE

    FALSE

    TINY_PROFILE

    Include tiny profiling info

    TRUE / FALSE

    FALSE

    COMM_PROFILE

    Include comm profiling info

    TRUE / FALSE

    FALSE

    TRACE_PROFILE

    Include trace profiling info

    TRUE / FALSE

    FALSE

    +
    +

    Note

    +

    Do not set both USE_OMP and USE_CUDA to true.

    +
    +

    Additional options and information on using other compilers can be found in the +AMReX documentation at +https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html .

    +
    3. +

  3. Make the executable:

    +

    Now type

    +
    make
+
    +
    +

    The name of the resulting executable (generated by the make system) encodes several of the build characteristics, including dimensionality of the problem, compiler name, and whether MPI and/or OpenMP were linked with the executable. +Thus, several different build configurations may coexist simultaneously in a problem folder. +For example, the default build in incflo/test_2d will look +like incflo2d.gnu.MPI.EB.ex, indicating that this is a 2-d version of the code, made with +COMP=gnu, USE_MPI=TRUE and support for embedded boundaries (EB).

    +
    4. +
+
+
+

Building with CMake

+

CMake build is a two-steps process. First cmake is invoked to create +configuration files and makefiles in a chosen directory (builddir). +Next, the actual build is performed by invoking make from within builddir. +The CMake build process is summarized as follows:

+
mkdir /path/to/builddir
+cd    /path/to/builddir
+cmake [options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] /path/to/incflo
+make
+
+
+

In the above snippet, [options] indicates one or more options for the +customization of the build, as described later in this section. +If the option CMAKE_BUILD_TYPE is omitted, +CMAKE_BUILD_TYPE=Release is assumed.

+

There are two modes to build incflo with CMake:

+
+

o SUPERBUILD (recommended): AMReX and AMReX-Hydro are built as part +of the incflo build process. This method is strongly encouraged as it +ensures that the configuration options are consistent.

+

o STANDALONE: incflo source code is built separately and linked to an existing +AMReX installation. This is ideal for continuous integration severs (CI) +and regression testing applications. AMReX library version and configuration options +must meet incflo requirements.

+
+
+

Note

+

incflo requires CMake 3.14 or higher.

+
+ +
+

STANDALONE instructions

+

For a stand alone build, incflo CMake will look for an existing +AMReX installation on the system and link the incflo binaries against it.

+
+

Building AMReX

+

First, make sure you’ve downloaded all the source codes (see Downloading the code).

+

Next, configure, build and install AMReX as follows:

+
> cd /path/to/amrex
+> mkdir build
+> cd build
+> cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel]  [amrex options] -DCMAKE_INSTALL_PREFIX:PATH=/absolute/path/to/installdir -DAMREX_HYDRO_HOME=/path/to/AMReX-Hydro/source/directory ..
+> make install
+
+
+

[amrex options] is a list of any of the AMReX configuration options listed in the +AMReX user guide - Building with CMake. +We suggest to always use the option -DUSE_XSDK_DEFAULTS=yes when building AMReX for incflo. AMREX_HYDRO_HOME is a CMake variable pointing to the top-level source directory of the AMReX-Hydro distribution you downloaded earlier

+
+
+

Building incflo

+

Build incflo:

+
> cd /path/to/incflo
+> mkdir build
+> cd build
+> cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [incflo options] -DAMReX_ROOT=/absolute/path/to/amrex/installdir ..
+> make -j
+
+
+

Passing -DAMReX_ROOT=/absolute/path/to/amrex/installdir instructs CMake to search +/absolute/path/to/amrex/installdir before searching system paths +for an available AMReX installation. +AMReX_ROOT can also be set as an environmental variable instead of passing it as a command line option.

+

[incflo options] indicates any of the configuration option listed in the table below.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Option name

Description

Possible values

Default +value

CMAKE_CXX_FLAGS

User-defined C++ flags

valid C++ +compiler flags

None

CMAKE_CUDA_FLAGS

User-defined CUDA flags

valid CUDA +compiler flags

None

INCFLO_DIM

Dimensionality of the build

2/3

3

INCFLO_MPI

Enable build with MPI

no/yes

yes

INCFLO_OMP

Enable build with OpenMP

no/yes

no

INCFLO_CUDA

Enable build with CUDA

no/yes

no

INCFLO_EB

Build Embedded Boundary +support

no/yes

no

INCFLO_HYPRE

Enable HYPRE support

no/yes

no

INCFLO_FPE

Build with Floating-Point +Exceptions checks

no/yes

no

+
+
+
+

Few more notes on building incflo

+

The system default C++ compiler can be overwritten as follows:

+
> cmake -DCMAKE_CXX_COMPILER=<c++-compiler>  [options]  ..
+
+
+

When building on a platform that uses the module utility, use either +the above command (with full path to the compilers) or the following:

+
> cmake -DCMAKE_CXX_COMPILER=CC [options] ..
+
+
+

incflo uses the same compiler flags used to build AMReX, unless +CMAKE_CXX_FLAGS is explicitly provided, or +the environmental variables CXXFLAGS is set.

+
+
+

Building incflo for Summit (OLCF)

+

For the Summit cluster at OLCF, you first need to load/unload modules required to build incflo.

+
> module unload xalt
+> module unload darshan
+> module load gcc
+> module load cmake/3.14.0
+
+
+

Now incflo can be built following the SUPERBUILD Instructions (recommended).

+

To build incflo for GPUs, you need to load cuda module:

+
> module load cuda/10.1.105
+
+
+

To compile for GPUs:

+
> cd incflo
+> mdkir build
+> cd build
+> cmake -DCMAKE_CXX_COMPILER=g++ -DINCFLO_CUDA=yes
+> make -j
+
+
+

An example of a submission_script for using the GPUs on Summit can be found in incflo/summit_script.sh. +For more information about Summit cluster: https://www.olcf.ornl.gov/for-users/system-user-guides/summit/

+
+
+
+

Running the code

+

incflo takes an input file as its first command-line argument. The file may +contain a set of parameter definitions that will override defaults set in the code. +Many example inputs files can be found in the incflo/test_XXX directories. +For example, to run the Taylor-Green vortices example in incflo/test_2d, assuming your executable is named incflo.ex +and is located in the test_2d directory, then you can simply type:

+
> cd incflo/test_2d
+> ./incflo.ex benchmark.taylor_green_vortices
+
+
+

For more information on inputs options, see the Run-time Inputs section.

+

incflo can generate subfolders in the current folder +named plt00000, plt00010, etc, and chk00000, +chk00010, etc. These are called plotfiles and checkpoint +files. The plotfiles are used for visualization of derived fields; the checkpoint +files are used for restarting the code. For more information see the AMReX Documentation on +I/O (Plotfile, Checkpoint).

+
+
+

Visualizing the Results

+

Options for visualizing the data are discussed in the AMReX Documenation on Visualization.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsAlgorithm.html b/InputsAlgorithm.html new file mode 100644 index 00000000..1e3c908a --- /dev/null +++ b/InputsAlgorithm.html @@ -0,0 +1,197 @@ + + + + + + + Algorithm Options — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Algorithm Options

+

The following inputs must be preceded by “incflo.”

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

advection_type

Advection scheme (options: Godunov, MOL, BDS)

string

Godunov

advect_momentum

Advect momentum (otherwise use convective differencing)

bool

false

advect_tracer

evolve the tracer equation(s)?

bool

false

ntrac

number of tracers

int

1

constant_density

Only evolve the continuity equation if false

bool

true

rho_0

density (if constant)

Real

1.0

diffusion_type

Diffusion type (0 = Explicit, 1 = Crank-Nicholson, 2 = Implicit)

int

2 (Implicit)

mu

viscosity (if constant)

Real

1.0

mu_s

scalar diffusivity

Real(s)

0.0

use_tensor_solve

In velocity solve, use multicomponent \(\nabla \cdot \tau\) +otherwise use separate solves for each velocity component

bool

true

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsCheckpoint.html b/InputsCheckpoint.html new file mode 100644 index 00000000..3fd93201 --- /dev/null +++ b/InputsCheckpoint.html @@ -0,0 +1,161 @@ + + + + + + + Checkpoint/Restart — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Checkpoint/Restart

+

The following inputs must be preceded by “amr” and control checkpoint/restart.

+ + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

restart

If present, then the name of file to restart from

String

None

check_int

Frequency of checkpoint output; +if -1 then no checkpoints will be written

Int

-1

check_file

Prefix to use for checkpoint output

String

chk

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsInitialization.html b/InputsInitialization.html new file mode 100644 index 00000000..b4ff1ae0 --- /dev/null +++ b/InputsInitialization.html @@ -0,0 +1,172 @@ + + + + + + + Initialization — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Initialization

+

The following inputs must be preceded by “amr” and determine how we initialize a calculation:

+ + + + + + + + + + + + + + + +

Description

Type

Default

restart

If set, then restart from this file rather than from scratch

String

None

+

The following inputs must be preceded by “incflo” and determine how we initialize a calculation:

+ + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

do_initial_proj

Should we do the initial projection?

Bool

True

initial_iterations

How many pressure iterations before starting the first timestep

Int

3

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsLoadBalancing.html b/InputsLoadBalancing.html new file mode 100644 index 00000000..53cfbb2c --- /dev/null +++ b/InputsLoadBalancing.html @@ -0,0 +1,204 @@ + + + + + + + Gridding and Load Balancing — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Gridding and Load Balancing

+

The following inputs must be preceded by “amr” and determine how we create the grids and how often we regrid. The most +commonly used options are listed here. See the AMReX documentation on Gridding and Load Balancing for additional +options.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

regrid_int

How often to regrid (in number of steps at level 0) +if regrid_int = -1 then no regridding will occur

Int

-1

max_grid_size_x

Maximum number of cells at level 0 in each grid in x-direction

Int

32

max_grid_size_y

Maximum number of cells at level 0 in each grid in y-direction

Int

32

max_grid_size_z

Maximum number of cells at level 0 in each grid in z-direction

Int

32

blocking_factor_x

Each grid must be divisible by blocking_factor_x in x-direction

Int

8

blocking_factor_y

Each grid must be divisible by blocking_factor_y in y-direction

Int

8

blocking_factor_z

Each grid must be divisible by blocking_factor_z in z-direction

Int

8

+

The following inputs must be preceded by “fabarray_mfiter” and determine how we create the logical tiles:

+ + + + + + + + + + + + + + + +

Description

Type

Default

tile_size

Maximum number of cells in each direction for (logical) tiles

+

(3D CPU-only)

+

IntVect

1024000

+

1024000,8,8

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsMultigrid.html b/InputsMultigrid.html new file mode 100644 index 00000000..311cb7e2 --- /dev/null +++ b/InputsMultigrid.html @@ -0,0 +1,209 @@ + + + + + + + Multigrid Inputs — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Multigrid Inputs

+

Below is a list of the most commonly used multigrid settings options. +To control the nodal projection precede with “nodal_proj”, for the MAC projection use “mac_proj”, and +for the diffusion solver use “diffusion”

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

verbose

Verbosity of multigrid solver

Int

0

bottom_verbose

Verbosity of BiCGStab solver

Int

0

rtol

Relative tolerance

+
Real
+
float
+
+
+
1.e-11
+
1.e-4
+
+

atol

Absolute tolerance

+
Real
+
float
+
+
+
1.e-14
+
1.e-7
+
+

maxiter

Maximum number of iterations

Int

nodal 100 +MAC 200 +diffusion 100

bottom_maxiter

Maximum number of iterations in the +bottom solver if using bicg, cg, bicgcg or cgbicg

Int

nodal 100 +MAC 200 +diffusion 100

mg_max_coarsening_level

Maximum number of coarser levels to allow. +If set to 0, the bottom solver will be called at the current level

Int

100

bottom_solver

Which bottom solver to use. +Options are bicgcg, bicgstab, cg, cgbicg, smoother or hypre

String

bicgcg

+

See AMReX-Hydro’s documentation on projections inputs for additional projection options.

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsPlotFiles.html b/InputsPlotFiles.html new file mode 100644 index 00000000..68f1aeb7 --- /dev/null +++ b/InputsPlotFiles.html @@ -0,0 +1,278 @@ + + + + + + + Plotfiles and Other Output — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Plotfiles and Other Output

+

The following inputs must be preceded by “amr” and control frequency and naming of plotfile generation as well +as whether the EB geometry should be written out.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

plot_int

+

plot_per_exact

+

plot_per_approx

+

Frequency of plotfile output; +if -1 then no plotfiles will be written at this frequency +Time period of plotfile output (exact); will modify dt +if -1 then no plotfiles will be written at this frequency +Time period of plotfile output (approximate); does not modify dt +if -1 then no plotfiles will be written at this frequency

Int

+

Real

+

Real

+

-1

+

-1

+

-1

+

plotfile_on_restart

Should we write a plotfile when we restart (only used if plot_int>0)

Bool

False

plot_file

Prefix to use for plotfile output

String

plt

write_eb_surface

Should we write out the EB geometry in vtp format +If true, it will only be written once,after initialization or restart

Bool

False

+

The following inputs must be preceded by “amr” and control what variables will be written in plotfiles.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

plt_ccse_regtest

Save all variables to plot file (overrides all other IO flags)

Int

0

plt_velx

Save x-velocity to plot file

Int

1

plt_vely

Save y-velocity to plot file

Int

1

plt_velz

Save z-velocity to plot file

Int

1

plt_p

Save pressure to plot file

Int

0

plt_rho

Save density to plot file

Int

0

plt_tracer

Save tracer to plot file

Int

0

plt_eta

Save viscosity to plot file

Int

0

plt_gpx

Save dp/dx to plot file

Int

1

plt_gpy

Save dp/dy to plot file

Int

1

plt_gpz

Save dp/dz to plot file

Int

1

plt_vort

Save vorticity to plot file

Int

1

plt_forcing

Save forcing term for velocity to plot file

Int

0

plt_strainrate

Save strain rate to plot file

Int

0

plt_divu

Save velocity divergence to plot file

Int

0

plt_vfrac

Save EB volume fraction to plot file

Int

1

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsProblemDefinition.html b/InputsProblemDefinition.html new file mode 100644 index 00000000..79b4ae1b --- /dev/null +++ b/InputsProblemDefinition.html @@ -0,0 +1,266 @@ + + + + + + + Problem Definition — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Problem Definition

+

The following inputs must be preceded by “amr.”

+ + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

n_cell

Number of cells at level 0 in each coordinate direction

Int Int Int

None

max_level

Maximum level of refinement allowed (0 when single-level)

Int

None

+

The following inputs must be preceded by “geometry.”

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

coord_sys

0 for Cartesian

Int

0

is_periodic

1 for true, 0 for false (one value for each coordinate direction)

Ints

0 0 0

prob_lo

Low corner of physical domain (physical not index space)

Reals

None

prob_hi

High corner of physical domain (physical not index space)

Reals

None

+

The following inputs must be preceded by “incflo.”

+ + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

geometry

Which type of EB geometry are we using?

String

gravity

Gravity vector (e.g., incflo.gravity = -9.81 0.0 0.0)

Reals

(0, 0, 0)

delp

Pressure drop (Pa)

Real

(0, 0, 0)

+

Setting basic boundary conditions can be specified by inputs preceded by “xlo”, “xhi”, “ylo”, “yhi”, “zlo”, and “zhi”

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

type

Used to define boundary type. Available options include:

+
    +

  • ‘pi’ or ‘pressure_inflow’

    • +

  • ‘po’ or ‘pressure_outflow’

    • +

  • ‘mi’ or ‘mass_inflow’

    • +

  • ‘nsw’ or ‘no_slip_wall’

    • +

  • ‘mixed’

    • +
+

String

None

pressure

Sets boundary pressure for pressure inflows, outflows and mass inflows

Real

None

velocity

Sets boundary velocity for mass inflows

Reals

(0, 0, 0)

density

Sets boundary density for mass inflows

Real

1.0

tracer

Sets boundary tracer for mass inflows

Real

0.0

+
+

The ‘mixed’ boundary type allows for inflow and outflow on the same domain face. +The implementation requires that there is EB separating the inflow and outflow regions, +and only currently treats constant viscosity (i.e. requires the inputs file contains incflo.use_tensor_solve = false). +It does allow for non-constant scalar diffusivity. To create a new problem setup with mixed BCs, one must additionally +specify the Dirchlet and Neumann areas in prob/prob_bc.cpp In this file there are functions to set the needed BC info for the diffusion solver, the MAC projection, and with the same function, the nodal projection and advection. Comments in the code provide a detailed explaination for each instance. For addditional details on mixed BCs, also see AMReX-Hydro’s documentation (Boundary conditions).

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsTimeStepping.html b/InputsTimeStepping.html new file mode 100644 index 00000000..d0a71753 --- /dev/null +++ b/InputsTimeStepping.html @@ -0,0 +1,205 @@ + + + + + + + Time Stepping — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Time Stepping

+

The first three inputs below do not take a prefix. Note that the first two are both specified, both criteria +are used and the simulation still stop when the first criterion is hit. In the case of unsteady flow, +the simulation will stop when either the number of steps reaches max_step or time reaches stop_time. +In the case of steady flow, the simulation will stop when either the tolerance (difference between +subsequent steps) is reached or the number of iterations reaches the maximum number specified.

+ + + + + + + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

max_step

Maximum number of time steps to take

Int

-1

stop_time

Maximum time to reach

Real

-1.0

steady_state

Is this a steady state problem?

Bool

False

+

The inputs below must be preceded by “incflo.”

+ + + + + + + + + + + + + + + + + + + + +

Description

Type

Default

fixed_dt

Value of fixed dt if > 0

Real

-1.

cfl

CFL constraint (dt < cfl * dx / u) if fixed_dt not > 0

Real

0.5

+
+

Setting the Time Step

+
+
    +

  • If you want to fix the dt, simply set incflo.fixed_dt = XXX and the fluid time +step will always be that number.

    • +

  • If you want to let the code determine the appropriate time step using the advective CFL +condition, then set incflo.cfl = 0.7 for example, and the fluid time step will +be computed to be dt = 0.7 * dx / max(vel).

    • +

  • Note that the cfl defaults to 0.5 so it does not have to be set in the inputs file. If neither +incflo.cfl nor fixed_dt is set, then default value of cfl will be used. +If incflo.fixed_dt is set, then it will override the cfl option whether +incflo.cfl is set or not.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InputsVerbosity.html b/InputsVerbosity.html new file mode 100644 index 00000000..ff6b90e1 --- /dev/null +++ b/InputsVerbosity.html @@ -0,0 +1,150 @@ + + + + + + + Verbosity — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Verbosity

+

The following inputs must be preceded by “incflo.”

+ + + + + + + + + + + + + + + +

Description

Type

Default

verbose

Verbosity in incflo routines

Int

0

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Inputs_Chapter.html b/Inputs_Chapter.html new file mode 100644 index 00000000..55822db1 --- /dev/null +++ b/Inputs_Chapter.html @@ -0,0 +1,145 @@ + + + + + + + Run-time Inputs — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+ +
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Introduction.html b/Introduction.html new file mode 100644 index 00000000..a1b44355 --- /dev/null +++ b/Introduction.html @@ -0,0 +1,146 @@ + + + + + + + Introduction — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Introduction

+

incflo is a massively parallel code for solving the incompressible Navier-Stokes +equations in 2-D or 3-D, with the option for an embedded boundary (cut cell) representation of +of complex geometries.

+

It is built on top of AMReX, a publicly available software framework designed for building +massively parallel block-structured adaptive mesh refinement (AMR) +applications. It also utilizes AMReX-Hydro, a set of routines that support the construction +of convective terms for incompressible and low Mach number flow modeling in cartesian coordinates +with (or without) embedded boundaries and R-Z coordinate systems.

+

Another AMReX-based code, IAMR, also solves the variable-density incompressible +Navier-Stokes equations in 2-D or 3-D but is based on a subcycling-in-time approach.

+

Key software and algorithmic features of incflo include:

+
    +

  • Fluid velocity, density and tracers are defined at cell centroids; pressure is defined at nodes.

    • +

  • Possible advection algorithms: a Method-Of-Lines (MOL) approach and a Godunov-method algorithm. +Both use an intermediate MAC projection for face-centered advection velocities

    • +

  • Incompressibility of the fluid is imposed through the use of a projection at the end of the time step

    • +

  • Implicit or explicit discretization of viscous terms with variable viscosity

    • +

  • The representation of the complex geometry uses the embedded boundary, or cut-cell, approach

    • +

  • Hybrid parallelization via MPI+X where X = OpenMP for multicore machines, and CUDA/HIP/DCP++ for CPU/GPU systems

    • +

  • Parallel I/O using AMReX native I/O or HDF5.

    • +

  • Plotfile format supported by AmrVis, VisIt, ParaView, and yt.

    • +
+

The incflo source code can be found at https://github.com/AMReX-Fluids/incflo/. +incflo heavily leverages AMReX (see https://amrex-codes.github.io/) which is supported by +ECP as part of the AMReX Co-Design Center.

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ManagingGridHierarchy_Chapter.html b/ManagingGridHierarchy_Chapter.html new file mode 100644 index 00000000..1ac3daa9 --- /dev/null +++ b/ManagingGridHierarchy_Chapter.html @@ -0,0 +1,135 @@ + + + + + + + Gridding and Load Balancing — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Gridding and Load Balancing

+

incflo leverages AMReX’s flexibility when it comes to how to decompose the +computational domain into individual rectangular grids, and how to distribute +those grids to MPI ranks. There can be grids of different sizes, +more than one grid per MPI rank, and different strategies for distributing the grids to MPI ranks.

+

AMReX’s docmumentation on Gridding and Load Balancing contains further details. +See Grid Creation for grids are created, i.e. how the BoxArray on which +MultiFabs will be built is defined at each level. +See Load Balancing for the strategies AMReX supports for distributing +grids to MPI ranks, i.e. defining the DistributionMapping with which +MultiFabs at that level will be built.

+

When running on multicore machines with OpenMP, we can also control the distribution of +work by setting the size of grid tiles (by defining fabarray.mfiter_tile_size). +We can also specify the strategy for assigning tiles to OpenMP threads. +See MFIter with Tiling for more about tiling.

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/TimeStep.html b/TimeStep.html new file mode 100644 index 00000000..2c1806ca --- /dev/null +++ b/TimeStep.html @@ -0,0 +1,208 @@ + + + + + + + Time Step — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Time Step

+

incflo has the option to treat advection using either the Method of Lines (MOL) or a Godunov +approach. +Here we discuss the basic workflow involved in a time step for each of these approaches. +For details on how the convective terms are constructed, see the AMReX-Hydro documentation on Advection schemes. +For details on the projections, see the AMReX-Hydro documentation on Projection Methods.

+
+

MOL

+

MOL requires predictor-corrector methodology to achieve second order accuracy. +In the predictor

+
    +

  • Define \(U^{MAC,n}\), the face-centered (staggered) MAC velocity which is used for advection, using \(U^n\)

    • +

  • Define an approximation to the new-time state, \((\rho U)^{\ast}\) by setting

    • +
+
+\[\begin{split}(\rho U)^{\ast} =& (\rho U)^n - +\Delta t \left( \nabla \cdot (\rho U^{MAC} U) + \nabla {p}^{n-1/2} \right) \\ &+ +\Delta t \left( \nabla \cdot \tau^n + \rho^{n+1/2} {\bf H}_U \right)\end{split}\]
+
    +

  • Project \(U^{\ast}\) by solving

    • +
+
+\[\nabla \cdot \frac{1}{\rho} \nabla \phi = \nabla \cdot \left( \frac{1}{\Delta t} +U^{\ast}+ \frac{1}{\rho} \nabla {p}^{n-1/2} \right)\]
+

then defining

+
+\[U^{\ast \ast} = U^{\ast} - \frac{\Delta t}{\rho} \nabla \phi\]
+

and

+
+\[{p}^{n+1/2, \ast} = \phi\]
+

In the corrector

+
    +

  • Define \(U^{MAC,\ast \ast}\) at the “new” time using \(U^{\ast \ast}\)

    • +

  • Define a new approximation to the new-time state, \((\rho U)^{\ast \ast \ast}\) by setting

    • +
+
+\[\begin{split}(\rho U)^{\ast \ast \ast} =& (\rho U)^n - \frac{\Delta t}{2} \left( \nabla \cdot (\rho U^{MAC} U)^n + \nabla \cdot (\rho U^{MAC} U)^{\ast \ast}\right) \\ +&+ \frac{\Delta t}{2} \left( \nabla \cdot \tau^n + \nabla \cdot \tau^{\ast \ast \ast} \right) + \Delta t \left( - \nabla {p}^{n+1/2,\ast} + \rho^{n+1/2} {\bf H}_U \right)\end{split}\]
+
    +

  • Project \(U^{\ast \ast \ast}\) by solving

    • +
+
+\[\nabla \cdot \frac{1}{\rho} \nabla \phi = \nabla \cdot \left( \frac{1}{\Delta t} U^{\ast \ast \ast} + \frac{1}{\rho} \nabla {p}^{n+1/2,\ast} \right)\]
+

then defining

+
+\[U^{n+1} = U^{\ast \ast \ast} - \frac{\Delta t}{\rho} \nabla \phi\]
+

and

+
+\[{p}^{n+1/2} = \phi\]
+
+
+

Godunov Methods

+

When we use a time-centered Godunov approach (i.e. the Godunov or BDS options), +we no longer need the predictor and corrector steps.

+
    +

  • Define the time-centered face-centered (staggered) MAC velocity which is used for advection: \(U^{MAC,n+1/2}\)

    • +

  • Define the new-time density, \(\rho^{n+1} = \rho^n - \Delta t (\rho^{n+1/2,pred} U^{MAC,n+1/2})\) by setting

    • +

  • Define an approximation to the new-time state, \((\rho U)^{\ast}\) by setting

    +
    +\[\begin{split}(\rho^{n+1} U^{\ast}) &= (\rho^n U^n) - +\Delta t \left( \nabla \cdot (\rho U^{MAC} U) + \nabla {p}^{n-1/2} \right) \\ +&+ \frac{\Delta t}{2} ( \nabla \cdot \tau^n + \nabla \cdot \tau^\ast) + + \Delta t \; \rho^{n+1/2} {\bf H}_U\end{split}\]
    +

    (for implicit diffusion, which is the current default)

    +
    • +

  • Project \(U^{\ast}\) by solving

    • +
+
+\[\nabla \cdot \frac{1}{\rho} \nabla \phi = \nabla \cdot \left( \frac{1}{\Delta t} +U^{\ast}+ \frac{1}{\rho} \nabla {p}^{n-1/2} \right)\]
+

then defining

+
+\[U^{n+1} = U^{\ast} - \frac{\Delta t}{\rho} \nabla \phi\]
+

and

+
+\[{p}^{n+1/2} = \phi\]
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/_sources/Debugging.rst.txt b/_sources/Debugging.rst.txt new file mode 100644 index 00000000..2e121468 --- /dev/null +++ b/_sources/Debugging.rst.txt @@ -0,0 +1,71 @@ +.. role:: cpp(code) + :language: c++ + +.. _Chap:Debugging: + +Debugging +========= + +Debugging is an art. Everyone has their own favorite method. Here we +offer a few tips we have found to be useful. + +Compiling in debug mode (e.g., :cpp:`make DEBUG=TRUE` for gmake users; +:cpp:`cmake -DDEBUG` for cmake users) and running with +:cpp:`amrex.fpe_trap_invalid=1` in the inputs file can be helpful. +In debug mode, many compiler debugging flags are turned on and all +:cpp:`MultiFab` s are initialized to signaling NaNs. The +:cpp:`amrex.fpe_trap_invalid` parameter will result in backtrace files +when a floating point exception occurs. One can then examine those +files to track down the origin of the issue. + +Several ways to look at the data include: + +1) Writing a :cpp:`MultiFab` to disk with + + .. highlight:: c++ + + :: + + VisMF::Write(const FabArray& mf, const std::string& name); + + and examining it with ``Amrvis`` (section :ref:`sec:amrvis` in the AMReX documentation). + +2) You can also use the :cpp:`print_state` routine: + + .. highlight:: c++ + + :: + + void print_state(const MultiFab& mf, const IntVect& cell, const int n=-1); + + which outputs the data for a single cell. + +3) If you want to compare old and new plotfiles, + + .. highlight:: c++ + + :: + + fcompare --infile1 plt00000_run1 --infile2 plt00000_run2 --diffvar u_g + + will print out the maximum absolute and relative differences between the two plotfiles + for each variable and will also create a new plotfile "diffs" that contains the difference + in u_g (in this case) between the two plotfiles. + + The :cpp:`fcompare` executable can be built in AMReX (go to amrex/Tools/Plotfile and type "make"). + +Valgrind is another useful debugging tool. Note that for runs using +more than one MPI process, one can tell valgrind to output to different +files for different processes. For example, + + .. highlight:: console + + :: + + mpiexec -n 4 valgrind --leak-check=yes --track-origins=yes --log-file=vallog.%p ./incflo.exe ... + + +Also see AMReX's documentation on :ref:`amrex:sec:basics:debugging` for further suggestions. + +If you believe you've encountered a bug or incorrect behavior in incflo, please report the issue +on incflo's github page `here `_ . diff --git a/_sources/EB.rst.txt b/_sources/EB.rst.txt new file mode 100644 index 00000000..73fed8b5 --- /dev/null +++ b/_sources/EB.rst.txt @@ -0,0 +1,36 @@ +.. role:: cpp(code) + :language: c++ + +.. role:: fortran(code) + :language: fortran + +.. _Chap:EB: + +Embedded Boundaries +=================== + +incflo follows AMReX's approach to embedded boundaries (EB), which is described in the +`AMReX EB documentation `_. +By default, incflo uses AMReX's constructive solid geometry framework defined in the namespace :cpp:`amrex::EB2`. +Alternatively, the constructive solid geometry can also be created using OpenSCAD's CSG file format by installing +the :cpp:`csg-eb` library. To use this option, incflo must be built with the flag +:cpp:`USE_CSG=TRUE` and :cpp:`CSGEB_HOME` must be set to where the library was installed. +See `MFIX's CSG-EB repository `_ for more details about this format. + +incflo provides several options of embedded boundary geometries. The inputs parameter ``incflo.geometry = XXX`` +determines which geometry is selected by :cpp:`incflo::MakeEBGeometry()` within :cpp:`incflo/src/embedded_boundaries`. +The procedure to create your own EB geometry is described in the AMReX documentation on :ref:`amrex:sec:EB:ebinit`. +As discussed in the AMReX documentation, note that when constructing the EB, we must specify a +maxium coarsening level (``max_crse_level``): + +.. highlight:: c++ + +:: + + EB2::Build(gshop, geom[lev], required_crse_lev, max_crse_level); + + +This specifies to which level of coarseness the EB is still defined. It might not be +immediately obvious, but the multigrid solver (used in the fluid solve) also +depends indirectly on this parameters. Choosing a value of ``max_crse_level`` that is too small might restrict +how many levels the MLMG solver can use, and therefore give slightly different answers in the fluid solve. diff --git a/_sources/FluidEquations.rst.txt b/_sources/FluidEquations.rst.txt new file mode 100644 index 00000000..03a8e470 --- /dev/null +++ b/_sources/FluidEquations.rst.txt @@ -0,0 +1,43 @@ +Fluid Variables +=============== + + +-----------------------+--------------------------------------------------+ + | Variable | Definition | + +=======================+==================================================+ + | :math:`\rho` | Fluid density | + +-----------------------+--------------------------------------------------+ + | :math:`U` | Fluid velocity | + +-----------------------+--------------------------------------------------+ + | :math:`\tau` | Viscous stress tensor | + +-----------------------+--------------------------------------------------+ + | :math:`\mu_s` | scalar diffusivity | + +-----------------------+--------------------------------------------------+ + | :math:`{\bf g}` | Gravitational acceleration | + +-----------------------+--------------------------------------------------+ + | :math:`{\bf H}_U` | :math:`= (H_x , H_y , H_z )`, External Forces | + +-----------------------+--------------------------------------------------+ + | :math:`H_s` | External sources | + +-----------------------+--------------------------------------------------+ + +Fluid Equations +=============== + +Conservation of fluid mass: + +.. math:: \frac{\partial \rho}{\partial t} + \nabla \cdot (\rho U) = 0 + +Conservation of fluid momentum: + +.. math:: \frac{ \partial (\rho U)}{\partial t} + + \nabla \cdot (\rho U U) + \nabla p = \nabla \cdot \tau + {\bf H}_U + +Incompressibility constraint: + +.. math:: \nabla \cdot U = 0 + +Tracer(s): + +.. math:: \frac{\partial \rho s}{\partial t} + \nabla \cdot (\rho U s) = \nabla \cdot \mu_s \nabla s + \rho H_s + +By default, :math:`H_s = 0` and :math:`{\bf H}_U = {\bf 0}`. +If gravity is set during runtime, then :math:`{\bf H}_U` defaults to :math:`\rho {\bf g}` diff --git a/_sources/Fluids_Chapter.rst.txt b/_sources/Fluids_Chapter.rst.txt new file mode 100644 index 00000000..535a91e1 --- /dev/null +++ b/_sources/Fluids_Chapter.rst.txt @@ -0,0 +1,12 @@ +.. _Chap:Fluids: + +Here we describe the fluid variables, the governing equations, and the time discretization +of the fluid evolution. + +Solving the Fluid Equations +=========================== + +.. toctree:: + + FluidEquations + TimeStep diff --git a/_sources/GettingStarted.rst.txt b/_sources/GettingStarted.rst.txt new file mode 100644 index 00000000..863aee58 --- /dev/null +++ b/_sources/GettingStarted.rst.txt @@ -0,0 +1,373 @@ +.. _Chap:GettingStarted: + +Getting Started +*************** +This section walks you through a brief introduction to using incflo. + +.. + alternative to `` `` is :code:` ` + + +.. _sec:Download: + +Downloading the code +==================== +incflo is built on top of the AMReX framework. In order to run +incflo, you must download separate git modules for incflo, AMReX +and AMReX-Hydro. + +First, make sure that git is installed on your machine. + +#. Download the AMReX repository by typing: + + .. code:: shell + + git clone https://github.com/AMReX-Codes/amrex.git + + This will create a folder called ``amrex/`` on your machine. + For additional information on downloading the AMReX source code see `AMReX user guide - Downloading the code `_. + + +#. Download the AMReX-Hydro repository by typing: + + .. code:: shell + + git clone https://github.com/AMReX-Fluids/AMReX-Hydro.git + + This will create a folder called ``AMReX-Hydro/`` on your machine. + +#. Download the incflo repository by typing: + + .. code:: shell + + git clone https://github.com/AMReX-Fluids/incflo.git + + This will create a folder called ``incflo/`` on your machine. + +You will want to periodically update each of these repositories +by typing ``git pull`` within each repository. + +Next, you can choose to either :ref:`sec:GNUMake` or :ref:`sec:CMake`. + + +.. _sec:GNUMake: + +Building with GNU Make +====================== + +Here, we walk you through compiling an incflo executable. +Decide whether you want to build the executable in 2-D vs 3-D, +with or without EB (embedded boundaries / cut cells), and choose the corresponding +directory: ``test_2d``, ``test_3d``, ``test_no_eb_2d``, or ``test_no_eb``. +For this example, let's say you want to build in 2-D with cut cells. +Then to build the code: + +#. ``cd`` to the desired build directory; e.g. + + .. code:: shell + + cd incflo/test_2d + + +#. Edit the ``GNUmakefile``: + + Set AMREX_HOME to be the path to the directory where you have put amrex. NOTE: when setting ``AMREX_HOME`` in the ``GNUmakefile``, be aware that ``~`` does not expand, so ``AMREX_HOME=~/amrex/`` will yield an error. + + Alternatively, the path to AMReX can be set up as an environment variable, ``AMREX_HOME``, on your machine to point to the path name where you have put AMReX. For example, if you are using the bash shell, you can add this to your ``.bashrc`` as: + + .. highlight:: bash + + :: + + export AMREX_HOME=/path/to/amrex + + alternatively, in tcsh one can set + + .. highlight:: tcsh + + :: + + setenv AMREX_HOME /path/to/amrex + + + Common options that you can set in the GNUMakefile include + + +-----------------+------------------------------+------------------+-------------+ + | Option name | Description | Possible values | Default | + | | | | value | + +=================+==============================+==================+=============+ + | COMP | Compiler (gnu or intel) | gnu / intel | None | + +-----------------+------------------------------+------------------+-------------+ + | USE_MPI | Whether to enable MPI | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | USE_OMP | Whether to enable OpenMP | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | USE_CUDA | Whether to enable CUDA | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | DEBUG | Whether to use DEBUG mode | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | PROFILE | Include profiling info | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | TINY_PROFILE | Include tiny profiling info | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | COMM_PROFILE | Include comm profiling info | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | TRACE_PROFILE | Include trace profiling info | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + + .. note:: + **Do not set both USE_OMP and USE_CUDA to true.** + + Additional options and information on using other compilers can be found in the + AMReX documentation at + https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html . + + +#. Make the executable: + + Now type + + .. code:: shell + + make + + The name of the resulting executable (generated by the make system) encodes several of the build characteristics, including dimensionality of the problem, compiler name, and whether MPI and/or OpenMP were linked with the executable. + Thus, several different build configurations may coexist simultaneously in a problem folder. + For example, the default build in ``incflo/test_2d`` will look + like ``incflo2d.gnu.MPI.EB.ex``, indicating that this is a 2-d version of the code, made with + ``COMP=gnu``, ``USE_MPI=TRUE`` and support for embedded boundaries (EB). + + +.. _sec:CMake: + +Building with CMake +=================== + +CMake build is a two-steps process. First ``cmake`` is invoked to create +configuration files and makefiles in a chosen directory (``builddir``). +Next, the actual build is performed by invoking ``make`` from within ``builddir``. +The CMake build process is summarized as follows: + +.. highlight:: console + +:: + + mkdir /path/to/builddir + cd /path/to/builddir + cmake [options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] /path/to/incflo + make + +In the above snippet, ``[options]`` indicates one or more options for the +customization of the build, as described later in this section. +If the option ``CMAKE_BUILD_TYPE`` is omitted, +``CMAKE_BUILD_TYPE=Release`` is assumed. + +There are two modes to build incflo with CMake: + + o **SUPERBUILD (recommended):** AMReX and AMReX-Hydro are built as part + of the incflo build process. This method is strongly encouraged as it + ensures that the configuration options are consistent. + + o **STANDALONE:** incflo source code is built separately and linked to an existing + AMReX installation. This is ideal for continuous integration severs (CI) + and regression testing applications. AMReX library version and configuration options + must meet incflo requirements. + + + +.. note:: + **incflo requires CMake 3.14 or higher.** + +.. _sec:build:superbuild: + +SUPERBUILD Instructions (recommended) +------------------------------------- + +In this mode, incflo CMake inherents AMReX CMake targets and configuration options, as well as AMReX-Hydro CMake targets; that is, incflo, AMReX and AMReX-Hydro are configured and built as a single entity. + +First, make sure you've downloaded all the source codes (see :ref:`sec:Download`). + +Next, build the incflo executable: + + .. code-block:: console + + > cd incflo + > mkdir build + > cd build + > cmake -DAMREX_HOME=/path/to/amrex/source/directory [amrex options] -DAMREX_HYDRO_HOME=/path/to/AMReX-Hydro/source/directory -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] .. + > make -j + + +where ``AMREX_HOME`` is a CMake variable pointing to the top-level source directory of the AMReX distribution you downloaded earlier; ``[amrex options]`` is a list of any of the AMReX configuration options listed in the `AMReX user guide - Building with CMake `_; ``AMREX_HYDRO_HOME`` is a CMake variable pointing to the top-level source directory of the AMReX-Hydro distribution you downloaded earlier; and ``..`` is the relative path pointing to the top-level source directory of incflo or this example. + + +.. _sec:build:standalone: + +**STANDALONE** instructions +--------------------------------------------------------------------- + +For a stand alone build, incflo CMake will look for an existing +AMReX installation on the system and link the incflo binaries against it. + +Building AMReX +~~~~~~~~~~~~~~~~~~~ + +First, make sure you've downloaded all the source codes (see :ref:`sec:Download`). + +Next, configure, build and install AMReX as follows: + +.. code:: shell + + > cd /path/to/amrex + > mkdir build + > cd build + > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [amrex options] -DCMAKE_INSTALL_PREFIX:PATH=/absolute/path/to/installdir -DAMREX_HYDRO_HOME=/path/to/AMReX-Hydro/source/directory .. + > make install + +``[amrex options]`` is a list of any of the AMReX configuration options listed in the +`AMReX user guide - Building with CMake `_. +We suggest to always use the option ``-DUSE_XSDK_DEFAULTS=yes`` when building AMReX for incflo. ``AMREX_HYDRO_HOME`` is a CMake variable pointing to the top-level source directory of the AMReX-Hydro distribution you downloaded earlier + + +Building incflo +~~~~~~~~~~~~~~~~~ + + +Build incflo: + +.. code:: shell + + > cd /path/to/incflo + > mkdir build + > cd build + > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [incflo options] -DAMReX_ROOT=/absolute/path/to/amrex/installdir .. + > make -j + + +Passing ``-DAMReX_ROOT=/absolute/path/to/amrex/installdir`` instructs CMake to search +``/absolute/path/to/amrex/installdir`` before searching system paths +for an available AMReX installation. +``AMReX_ROOT`` can also be set as an environmental variable instead of passing it as a command line option. + + +``[incflo options]`` indicates any of the configuration option listed in the table below. + ++-----------------+------------------------------+------------------+-------------+ +| Option name | Description | Possible values | Default | +| | | | value | ++=================+==============================+==================+=============+ +| CMAKE\_CXX\ | User-defined C++ flags | valid C++ | None | +| _FLAGS | | compiler flags | | ++-----------------+------------------------------+------------------+-------------+ +| CMAKE\_CUDA\ | User-defined CUDA flags | valid CUDA | None | +| _FLAGS | | compiler flags | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_DIM | Dimensionality of the build | 2/3 | 3 | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_MPI | Enable build with MPI | no/yes | yes | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_OMP | Enable build with OpenMP | no/yes | no | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_CUDA | Enable build with CUDA | no/yes | no | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_EB | Build Embedded Boundary | no/yes | no | +| | support | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_HYPRE | Enable HYPRE support | no/yes | no | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_FPE | Build with Floating-Point | no/yes | no | +| | Exceptions checks | | | ++-----------------+------------------------------+------------------+-------------+ + + + + +Few more notes on building incflo +----------------------------------- + +The system default C++ compiler can be overwritten as follows: + +.. code:: shell + + > cmake -DCMAKE_CXX_COMPILER= [options] .. + +When building on a platform that uses the ``module`` utility, use either +the above command (with full path to the compilers) or the following: + +.. code:: shell + + > cmake -DCMAKE_CXX_COMPILER=CC [options] .. + +incflo uses the same compiler flags used to build AMReX, unless +``CMAKE_CXX_FLAGS`` is explicitly provided, or +the environmental variables ``CXXFLAGS`` is set. + + + +Building incflo for Summit (OLCF) +----------------------------------- + +For the Summit cluster at OLCF, you first need to load/unload modules required to build incflo. + +.. code:: shell + + > module unload xalt + > module unload darshan + > module load gcc + > module load cmake/3.14.0 + +Now incflo can be built following the :ref:`sec:build:superbuild`. + +To build incflo for GPUs, you need to load cuda module: + +.. code:: shell + + > module load cuda/10.1.105 + +To compile for GPUs: + +.. code:: shell + + > cd incflo + > mdkir build + > cd build + > cmake -DCMAKE_CXX_COMPILER=g++ -DINCFLO_CUDA=yes + > make -j + +An example of a *submission_script* for using the GPUs on Summit can be found in ``incflo/summit_script.sh``. +For more information about Summit cluster: ``_ + + +Running the code +================ +incflo takes an input file as its first command-line argument. The file may +contain a set of parameter definitions that will override defaults set in the code. +Many example inputs files can be found in the ``incflo/test_XXX`` directories. +For example, to run the Taylor-Green vortices example in ``incflo/test_2d``, assuming your executable is named ``incflo.ex`` +and is located in the ``test_2d`` directory, then you can simply type: + +.. code:: shell + + > cd incflo/test_2d + > ./incflo.ex benchmark.taylor_green_vortices + + +For more information on inputs options, see the :ref:`Chap:Inputs` section. + +incflo can generate subfolders in the current folder +named ``plt00000``, ``plt00010``, etc, and ``chk00000``, +``chk00010``, etc. These are called plotfiles and checkpoint +files. The plotfiles are used for visualization of derived fields; the checkpoint +files are used for restarting the code. For more information see the AMReX Documentation on +:ref:`amrex:Chap:IO`. + + +Visualizing the Results +======================= + +Options for visualizing the data are discussed in the AMReX Documenation on :ref:`amrex:Chap:Visualization`. diff --git a/_sources/InputsAlgorithm.rst.txt b/_sources/InputsAlgorithm.rst.txt new file mode 100644 index 00000000..29ee6c54 --- /dev/null +++ b/_sources/InputsAlgorithm.rst.txt @@ -0,0 +1,32 @@ +.. _Chap:InputsAlgorithm: + +Algorithm Options +================= + +The following inputs must be preceded by "incflo." + ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+==============+ +| advection_type | Advection scheme (options: Godunov, MOL, BDS) | string | Godunov | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| advect_momentum | Advect momentum (otherwise use convective differencing) | bool | false | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| advect_tracer | evolve the tracer equation(s)? | bool | false | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| ntrac | number of tracers | int | 1 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| constant_density | Only evolve the continuity equation if false | bool | true | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| rho_0 | density (if constant) | Real | 1.0 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| diffusion_type | Diffusion type (0 = Explicit, 1 = Crank-Nicholson, 2 = Implicit) | int | 2 (Implicit) | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| mu | viscosity (if constant) | Real | 1.0 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| mu_s | scalar diffusivity | Real(s) | 0.0 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| use_tensor_solve | In velocity solve, use multicomponent :math:`\nabla \cdot \tau` | bool | true | +| | otherwise use separate solves for each velocity component | | | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ + diff --git a/_sources/InputsCheckpoint.rst.txt b/_sources/InputsCheckpoint.rst.txt new file mode 100644 index 00000000..13bae0e4 --- /dev/null +++ b/_sources/InputsCheckpoint.rst.txt @@ -0,0 +1,18 @@ +.. _Chap:InputsCheckpoint: + +Checkpoint/Restart +================== + +The following inputs must be preceded by "amr" and control checkpoint/restart. + ++------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++==================+=======================================================================+=============+===========+ +| restart | If present, then the name of file to restart from | String | None | ++------------------+-----------------------------------------------------------------------+-------------+-----------+ +| check_int | Frequency of checkpoint output; | Int | -1 | +| | if -1 then no checkpoints will be written | | | ++------------------+-----------------------------------------------------------------------+-------------+-----------+ +| check_file | Prefix to use for checkpoint output | String | chk | ++------------------+-----------------------------------------------------------------------+-------------+-----------+ + diff --git a/_sources/InputsInitialization.rst.txt b/_sources/InputsInitialization.rst.txt new file mode 100644 index 00000000..9803a5e7 --- /dev/null +++ b/_sources/InputsInitialization.rst.txt @@ -0,0 +1,23 @@ +.. _Chap:InputsInitialization: + +Initialization +============== + +The following inputs must be preceded by "amr" and determine how we initialize a calculation: + ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+==============+ +| restart | If set, then restart from this file rather than from scratch | String | None | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ + + +The following inputs must be preceded by "incflo" and determine how we initialize a calculation: + ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+==============+ +| do_initial_proj | Should we do the initial projection? | Bool | True | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| initial_iterations | How many pressure iterations before starting the first timestep | Int | 3 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ diff --git a/_sources/InputsLoadBalancing.rst.txt b/_sources/InputsLoadBalancing.rst.txt new file mode 100644 index 00000000..1e6d2333 --- /dev/null +++ b/_sources/InputsLoadBalancing.rst.txt @@ -0,0 +1,37 @@ +.. _Chap:InputsLoadBalancing: + +Gridding and Load Balancing +=========================== + +The following inputs must be preceded by "amr" and determine how we create the grids and how often we regrid. The most +commonly used options are listed here. See the AMReX documentation on :ref:`amrex:Chap:InputsLoadBalancing` for additional +options. + ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+===========+ +| regrid_int | How often to regrid (in number of steps at level 0) | Int | -1 | +| | if regrid_int = -1 then no regridding will occur | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| max_grid_size_x | Maximum number of cells at level 0 in each grid in x-direction | Int | 32 | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| max_grid_size_y | Maximum number of cells at level 0 in each grid in y-direction | Int | 32 | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| max_grid_size_z | Maximum number of cells at level 0 in each grid in z-direction | Int | 32 | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| blocking_factor_x | Each grid must be divisible by blocking_factor_x in x-direction | Int | 8 | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| blocking_factor_y | Each grid must be divisible by blocking_factor_y in y-direction | Int | 8 | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| blocking_factor_z | Each grid must be divisible by blocking_factor_z in z-direction | Int | 8 | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ + +The following inputs must be preceded by "fabarray_mfiter" and determine how we create the logical tiles: + ++----------------------+-----------------------------------------------------------------------+----------+-------------+ +| | Description | Type | Default | ++======================+=======================================================================+==========+=============+ +| tile_size | Maximum number of cells in each direction for (logical) tiles | IntVect | 1024000 | +| | | | | +| | (3D CPU-only) | | 1024000,8,8 | ++----------------------+-----------------------------------------------------------------------+----------+-------------+ diff --git a/_sources/InputsMultigrid.rst.txt b/_sources/InputsMultigrid.rst.txt new file mode 100644 index 00000000..07bfcc6c --- /dev/null +++ b/_sources/InputsMultigrid.rst.txt @@ -0,0 +1,38 @@ +.. _Chap:InputsMultigrid: + +Multigrid Inputs +================ + +Below is a list of the most commonly used multigrid settings options. +To control the nodal projection precede with "nodal_proj", for the MAC projection use "mac_proj", and +for the diffusion solver use "diffusion" + ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| | Description | Type | Default | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| verbose | Verbosity of multigrid solver | Int | 0 | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| bottom_verbose | Verbosity of BiCGStab solver | Int | 0 | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| rtol | Relative tolerance | | Real | | 1.e-11 | +| | | | float | | 1.e-4 | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| atol | Absolute tolerance | | Real | | 1.e-14 | +| | | | float | | 1.e-7 | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| maxiter | Maximum number of iterations | Int | nodal 100 | +| | | | MAC 200 | +| | | | diffusion 100 | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| bottom_maxiter | Maximum number of iterations in the | Int | nodal 100 | +| | bottom solver if using bicg, cg, bicgcg or cgbicg | | MAC 200 | +| | | | diffusion 100 | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| mg_max_coarsening_level | Maximum number of coarser levels to allow. | Int | 100 | +| | If set to 0, the bottom solver will be called at the current level | | | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ +| bottom_solver | Which bottom solver to use. | String | bicgcg | +| | Options are bicgcg, bicgstab, cg, cgbicg, smoother or hypre | | | ++-------------------------+-----------------------------------------------------------------------+-------------+----------------+ + +See AMReX-Hydro's documentation on :ref:`projections inputs ` for additional projection options. diff --git a/_sources/InputsPlotFiles.rst.txt b/_sources/InputsPlotFiles.rst.txt new file mode 100644 index 00000000..d3966a9a --- /dev/null +++ b/_sources/InputsPlotFiles.rst.txt @@ -0,0 +1,64 @@ +.. _Chap:InputsPlotfiles: + +Plotfiles and Other Output +========================== + +The following inputs must be preceded by "amr" and control frequency and naming of plotfile generation as well +as whether the EB geometry should be written out. + ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++=====================+=======================================================================+=============+===========+ +| plot_int | Frequency of plotfile output; | Int | -1 | +| | if -1 then no plotfiles will be written at this frequency | | | +| plot_per_exact | Time period of plotfile output (exact); will modify dt | Real | -1 | +| | if -1 then no plotfiles will be written at this frequency | | | +| plot_per_approx | Time period of plotfile output (approximate); does not modify dt | Real | -1 | +| | if -1 then no plotfiles will be written at this frequency | | | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plotfile_on_restart | Should we write a plotfile when we restart (only used if plot_int>0) | Bool | False | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plot_file | Prefix to use for plotfile output | String | plt | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| write_eb_surface | Should we write out the EB geometry in vtp format | Bool | False | +| | If true, it will only be written once,after initialization or restart | | | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ + +The following inputs must be preceded by "amr" and control what variables will be written in plotfiles. + ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++=====================+=======================================================================+=============+===========+ +| plt_ccse_regtest | Save all variables to plot file (overrides all other IO flags) | Int | 0 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_velx | Save x-velocity to plot file | Int | 1 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_vely | Save y-velocity to plot file | Int | 1 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_velz | Save z-velocity to plot file | Int | 1 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_p | Save pressure to plot file | Int | 0 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_rho | Save density to plot file | Int | 0 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_tracer | Save tracer to plot file | Int | 0 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_eta | Save viscosity to plot file | Int | 0 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_gpx | Save dp/dx to plot file | Int | 1 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_gpy | Save dp/dy to plot file | Int | 1 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_gpz | Save dp/dz to plot file | Int | 1 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_vort | Save vorticity to plot file | Int | 1 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_forcing | Save forcing term for velocity to plot file | Int | 0 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_strainrate | Save strain rate to plot file | Int | 0 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_divu | Save velocity divergence to plot file | Int | 0 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ +| plt_vfrac | Save EB volume fraction to plot file | Int | 1 | ++---------------------+-----------------------------------------------------------------------+-------------+-----------+ diff --git a/_sources/InputsProblemDefinition.rst.txt b/_sources/InputsProblemDefinition.rst.txt new file mode 100644 index 00000000..477c99cf --- /dev/null +++ b/_sources/InputsProblemDefinition.rst.txt @@ -0,0 +1,74 @@ +Problem Definition +================== + +The following inputs must be preceded by "amr." + ++-------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++===================+=======================================================================+=============+===========+ +| n_cell | Number of cells at level 0 in each coordinate direction | Int Int Int | None | ++-------------------+-----------------------------------------------------------------------+-------------+-----------+ +| max_level | Maximum level of refinement allowed (0 when single-level) | Int | None | ++-------------------+-----------------------------------------------------------------------+-------------+-----------+ + +The following inputs must be preceded by "geometry." + ++-----------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++=================+=======================================================================+=============+===========+ +| coord_sys | 0 for Cartesian | Int | 0 | ++-----------------+-----------------------------------------------------------------------+-------------+-----------+ +| is_periodic | 1 for true, 0 for false (one value for each coordinate direction) | Ints | 0 0 0 | ++-----------------+-----------------------------------------------------------------------+-------------+-----------+ +| prob_lo | Low corner of physical domain (physical not index space) | Reals | None | ++-----------------+-----------------------------------------------------------------------+-------------+-----------+ +| prob_hi | High corner of physical domain (physical not index space) | Reals | None | ++-----------------+-----------------------------------------------------------------------+-------------+-----------+ + + +The following inputs must be preceded by "incflo." + ++----------------------+-------------------------------------------------------------------------+----------+-----------+ +| | Description | Type | Default | ++======================+=========================================================================+==========+===========+ +| geometry | Which type of EB geometry are we using? | String | | ++----------------------+-------------------------------------------------------------------------+----------+-----------+ +| gravity | Gravity vector (e.g., incflo.gravity = -9.81 0.0 0.0) | Reals | (0, 0, 0) | ++----------------------+-------------------------------------------------------------------------+----------+-----------+ +| delp | Pressure drop (Pa) | Real | (0, 0, 0) | ++----------------------+-------------------------------------------------------------------------+----------+-----------+ + + +Setting basic boundary conditions can be specified by inputs preceded by "xlo", "xhi", "ylo", "yhi", "zlo", and "zhi" + ++--------------------+---------------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++====================+===========================================================================+=============+===========+ +| type | Used to define boundary type. Available options include: | String | None | +| | | | | +| | * 'pi' or 'pressure_inflow' | | | +| | * 'po' or 'pressure_outflow' | | | +| | * 'mi' or 'mass_inflow' | | | +| | * 'nsw' or 'no_slip_wall' | | | +| | * 'mixed' | | | ++--------------------+---------------------------------------------------------------------------+-------------+-----------+ +| pressure | Sets boundary pressure for pressure inflows, outflows and mass inflows | Real | None | ++--------------------+---------------------------------------------------------------------------+-------------+-----------+ +| velocity | Sets boundary velocity for mass inflows | Reals | (0, 0, 0) | ++--------------------+---------------------------------------------------------------------------+-------------+-----------+ +| density | Sets boundary density for mass inflows | Real | 1.0 | ++--------------------+---------------------------------------------------------------------------+-------------+-----------+ +| tracer | Sets boundary tracer for mass inflows | Real | 0.0 | ++--------------------+---------------------------------------------------------------------------+-------------+-----------+ + + The 'mixed' boundary type allows for inflow and outflow on the same domain face. + The implementation requires that there is EB separating the inflow and outflow regions, + and only currently treats constant viscosity (i.e. requires the inputs file contains ``incflo.use_tensor_solve = false``). + It does allow for non-constant scalar diffusivity. To create a new problem setup with mixed BCs, one must additionally + specify the Dirchlet and Neumann areas in ``prob/prob_bc.cpp`` In this file there are functions to set the needed BC info for the diffusion solver, the MAC projection, and with the same function, the nodal projection and advection. Comments in the code provide a detailed explaination for each instance. For addditional details on mixed BCs, also see AMReX-Hydro's documentation (:ref:`bcs`). + +.. + To create a new setup: + initial conditions go in prob/prob_init_fluid.cpp + inflow boundary conditions are set in prob/prob_bc.H -- the BCType for mixed bc is set at foextrap here to allow the outflow to get appropriately filled, which would already have happened before reaching these functions. + diff --git a/_sources/InputsTimeStepping.rst.txt b/_sources/InputsTimeStepping.rst.txt new file mode 100644 index 00000000..3fb6c3a2 --- /dev/null +++ b/_sources/InputsTimeStepping.rst.txt @@ -0,0 +1,45 @@ +.. sec:InputsTimeStepping: + +Time Stepping +============= + +The first three inputs below do not take a prefix. Note that the first two are both specified, both criteria +are used and the simulation still stop when the first criterion is hit. In the case of unsteady flow, +the simulation will stop when either the number of steps reaches max_step or time reaches stop_time. +In the case of steady flow, the simulation will stop when either the tolerance (difference between +subsequent steps) is reached or the number of iterations reaches the maximum number specified. + ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+==============+ +| max_step | Maximum number of time steps to take | Int | -1 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| stop_time | Maximum time to reach | Real | -1.0 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| steady_state | Is this a steady state problem? | Bool | False | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ + +The inputs below must be preceded by "incflo." + ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+==============+ +| fixed_dt | Value of fixed dt if > 0 | Real | -1. | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| cfl | CFL constraint (dt < cfl * dx / u) if fixed_dt not > 0 | Real | 0.5 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ + +Setting the Time Step +--------------------- + + * If you want to fix the dt, simply set :cpp:`incflo.fixed_dt = XXX` and the fluid time + step will always be that number. + + * If you want to let the code determine the appropriate time step using the advective CFL + condition, then set :cpp:`incflo.cfl = 0.7` for example, and the fluid time step will + be computed to be dt = 0.7 * dx / max(vel). + + * Note that the cfl defaults to 0.5 so it does not have to be set in the inputs file. If neither + :cpp:`incflo.cfl` nor :cpp:`fixed_dt` is set, then default value of cfl will be used. + If :cpp:`incflo.fixed_dt` is set, then it will override the cfl option whether + :cpp:`incflo.cfl` is set or not. diff --git a/_sources/InputsVerbosity.rst.txt b/_sources/InputsVerbosity.rst.txt new file mode 100644 index 00000000..1f8ae61b --- /dev/null +++ b/_sources/InputsVerbosity.rst.txt @@ -0,0 +1,13 @@ +.. _Chap:InputsVerbosity: + +Verbosity +========= + +The following inputs must be preceded by "incflo." + ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+==============+ +| verbose | Verbosity in incflo routines | Int | 0 | ++----------------------+-----------------------------------------------------------------------+-------------+--------------+ + diff --git a/_sources/Inputs_Chapter.rst.txt b/_sources/Inputs_Chapter.rst.txt new file mode 100644 index 00000000..c8f2c466 --- /dev/null +++ b/_sources/Inputs_Chapter.rst.txt @@ -0,0 +1,17 @@ +.. _Chap:Inputs: + +Run-time Inputs +=============== + +.. toctree:: + :maxdepth: 1 + + InputsProblemDefinition + InputsTimeStepping + InputsInitialization + InputsLoadBalancing + InputsMultigrid + InputsPlotFiles + InputsCheckpoint + InputsVerbosity + InputsAlgorithm diff --git a/_sources/Introduction.rst.txt b/_sources/Introduction.rst.txt new file mode 100644 index 00000000..4dc3ac22 --- /dev/null +++ b/_sources/Introduction.rst.txt @@ -0,0 +1,38 @@ +Introduction +============ + +incflo is a massively parallel code for solving the incompressible Navier-Stokes +equations in 2-D or 3-D, with the option for an embedded boundary (cut cell) representation of +of complex geometries. + +It is built on top of :ref:`AMReX `, a publicly available software framework designed for building +massively parallel block-structured adaptive mesh refinement (AMR) +applications. It also utilizes :ref:`AMReX-Hydro `, a set of routines that support the construction +of convective terms for incompressible and low Mach number flow modeling in cartesian coordinates +with (or without) embedded boundaries and R-Z coordinate systems. + +Another AMReX-based code, :ref:`IAMR `, also solves the variable-density incompressible +Navier-Stokes equations in 2-D or 3-D but is based on a subcycling-in-time approach. + +Key software and algorithmic features of incflo include: + +- Fluid velocity, density and tracers are defined at cell centroids; pressure is defined at nodes. + +- Possible advection algorithms: a Method-Of-Lines (MOL) approach and a Godunov-method algorithm. + Both use an intermediate MAC projection for face-centered advection velocities + +- Incompressibility of the fluid is imposed through the use of a projection at the end of the time step + +- Implicit or explicit discretization of viscous terms with variable viscosity + +- The representation of the complex geometry uses the embedded boundary, or cut-cell, approach + +- Hybrid parallelization via MPI+X where X = OpenMP for multicore machines, and CUDA/HIP/DCP++ for CPU/GPU systems + +- Parallel I/O using AMReX native I/O or HDF5. + +- Plotfile format supported by AmrVis, VisIt, ParaView, and yt. + +The incflo source code can be found at https://github.com/AMReX-Fluids/incflo/. +incflo heavily leverages AMReX (see https://amrex-codes.github.io/) which is supported by +ECP as part of the AMReX Co-Design Center. diff --git a/_sources/ManagingGridHierarchy_Chapter.rst.txt b/_sources/ManagingGridHierarchy_Chapter.rst.txt new file mode 100644 index 00000000..ec5c8f08 --- /dev/null +++ b/_sources/ManagingGridHierarchy_Chapter.rst.txt @@ -0,0 +1,22 @@ +.. role:: cpp(code) + :language: c++ + +Gridding and Load Balancing +=========================== + +incflo leverages AMReX's flexibility when it comes to how to decompose the +computational domain into individual rectangular grids, and how to distribute +those grids to MPI ranks. There can be grids of different sizes, +more than one grid per MPI rank, and different strategies for distributing the grids to MPI ranks. + +AMReX's docmumentation on :ref:`amrex:Chap:ManagingGridHierarchy` contains further details. +See :ref:`amrex:sec:grid_creation` for grids are created, i.e. how the :cpp:`BoxArray` on which +:cpp:`MultiFabs` will be built is defined at each level. +See :ref:`amrex:sec:load_balancing` for the strategies AMReX supports for distributing +grids to MPI ranks, i.e. defining the :cpp:`DistributionMapping` with which +:cpp:`MultiFabs` at that level will be built. + +When running on multicore machines with OpenMP, we can also control the distribution of +work by setting the size of grid tiles (by defining :cpp:`fabarray.mfiter_tile_size`). +We can also specify the strategy for assigning tiles to OpenMP threads. +See :ref:`amrex:sec:basics:mfiter:tiling` for more about tiling. diff --git a/_sources/TimeStep.rst.txt b/_sources/TimeStep.rst.txt new file mode 100644 index 00000000..e0aff06c --- /dev/null +++ b/_sources/TimeStep.rst.txt @@ -0,0 +1,89 @@ +Time Step +========= + +incflo has the option to treat advection using either the Method of Lines (MOL) or a Godunov +approach. +Here we discuss the basic workflow involved in a time step for each of these approaches. +For details on how the convective terms are constructed, see the AMReX-Hydro documentation on :ref:`hydro:schemes`. +For details on the projections, see the AMReX-Hydro documentation on :ref:`hydro:projections`. + +MOL +~~~~~~~~~~~~~~~~ + +MOL requires predictor-corrector methodology to achieve second order accuracy. +In the predictor + +- Define :math:`U^{MAC,n}`, the face-centered (staggered) MAC velocity which is used for advection, using :math:`U^n` + +- Define an approximation to the new-time state, :math:`(\rho U)^{\ast}` by setting + +.. math:: (\rho U)^{\ast} =& (\rho U)^n - + \Delta t \left( \nabla \cdot (\rho U^{MAC} U) + \nabla {p}^{n-1/2} \right) \\ &+ + \Delta t \left( \nabla \cdot \tau^n + \rho^{n+1/2} {\bf H}_U \right) + +- Project :math:`U^{\ast}` by solving + +.. math:: \nabla \cdot \frac{1}{\rho} \nabla \phi = \nabla \cdot \left( \frac{1}{\Delta t} + U^{\ast}+ \frac{1}{\rho} \nabla {p}^{n-1/2} \right) + +then defining + +.. math:: U^{\ast \ast} = U^{\ast} - \frac{\Delta t}{\rho} \nabla \phi + +and + +.. math:: {p}^{n+1/2, \ast} = \phi + + +In the corrector + +- Define :math:`U^{MAC,\ast \ast}` at the "new" time using :math:`U^{\ast \ast}` + +- Define a new approximation to the new-time state, :math:`(\rho U)^{\ast \ast \ast}` by setting + +.. math:: (\rho U)^{\ast \ast \ast} =& (\rho U)^n - \frac{\Delta t}{2} \left( \nabla \cdot (\rho U^{MAC} U)^n + \nabla \cdot (\rho U^{MAC} U)^{\ast \ast}\right) \\ + &+ \frac{\Delta t}{2} \left( \nabla \cdot \tau^n + \nabla \cdot \tau^{\ast \ast \ast} \right) + \Delta t \left( - \nabla {p}^{n+1/2,\ast} + \rho^{n+1/2} {\bf H}_U \right) + +- Project :math:`U^{\ast \ast \ast}` by solving + +.. math:: \nabla \cdot \frac{1}{\rho} \nabla \phi = \nabla \cdot \left( \frac{1}{\Delta t} U^{\ast \ast \ast} + \frac{1}{\rho} \nabla {p}^{n+1/2,\ast} \right) + +then defining + +.. math:: U^{n+1} = U^{\ast \ast \ast} - \frac{\Delta t}{\rho} \nabla \phi + +and + +.. math:: {p}^{n+1/2} = \phi + +Godunov Methods +~~~~~~~~~~~~~~~~~~~~ + +When we use a time-centered Godunov approach (i.e. the ``Godunov`` or ``BDS`` options), +we no longer need the predictor and corrector steps. + +- Define the time-centered face-centered (staggered) MAC velocity which is used for advection: :math:`U^{MAC,n+1/2}` + +- Define the new-time density, :math:`\rho^{n+1} = \rho^n - \Delta t (\rho^{n+1/2,pred} U^{MAC,n+1/2})` by setting + +- Define an approximation to the new-time state, :math:`(\rho U)^{\ast}` by setting + + .. math:: (\rho^{n+1} U^{\ast}) &= (\rho^n U^n) - + \Delta t \left( \nabla \cdot (\rho U^{MAC} U) + \nabla {p}^{n-1/2} \right) \\ + &+ \frac{\Delta t}{2} ( \nabla \cdot \tau^n + \nabla \cdot \tau^\ast) + + \Delta t \; \rho^{n+1/2} {\bf H}_U + + (for implicit diffusion, which is the current default) + +- Project :math:`U^{\ast}` by solving + +.. math:: \nabla \cdot \frac{1}{\rho} \nabla \phi = \nabla \cdot \left( \frac{1}{\Delta t} + U^{\ast}+ \frac{1}{\rho} \nabla {p}^{n-1/2} \right) + +then defining + +.. math:: U^{n+1} = U^{\ast} - \frac{\Delta t}{\rho} \nabla \phi + +and + +.. math:: {p}^{n+1/2} = \phi diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 00000000..fda3f269 --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,25 @@ +.. _incflo_doc_indx: + +Welcome to incflo's documentation! +==================================== + +incflo is an AMReX-based simulation code for modeling +the variable density incompressible Navier-Stokes equations in the presence +of complex geometries. It includes adaptive mesh refinement (AMR) +but without subcycling in time. + +For an AMReX-based incompressible flow code with subcycling in time, please see `IAMR `_ + +Active development in incflo is ongoing in the development branch. + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + Introduction + GettingStarted + Inputs_Chapter + ManagingGridHierarchy_Chapter + Fluids_Chapter + EB + Debugging diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */ +.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */ +.highlight .sx { color: #c65d09 } /* Literal.String.Other */ +.highlight .sr { color: #235388 } /* Literal.String.Regex */ +.highlight .s1 { color: #4070a0 } /* Literal.String.Single */ +.highlight .ss { color: #517918 } /* Literal.String.Symbol */ +.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #06287e } /* Name.Function.Magic */ +.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */ +.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */ +.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */ +.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */ +.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 00000000..7918c3fa --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,574 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/theme_overrides.css b/_static/theme_overrides.css new file mode 100644 index 00000000..78432dcd --- /dev/null +++ b/_static/theme_overrides.css @@ -0,0 +1,10 @@ +/* override table width restrictions */ +.wy-table-responsive table td, .wy-table-responsive table th { + white-space: normal; +} + +.wy-table-responsive { + margin-bottom: 24px; + max-width: 100%; + overflow: visible; +} \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 00000000..b1a2fc94 --- /dev/null +++ b/genindex.html @@ -0,0 +1,117 @@ + + + + + + Index — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+
+ +
+ +
+

© Copyright 2017-2018, Incflo Team.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html index b3bedfe9..d6ade470 100644 --- a/index.html +++ b/index.html @@ -1,102 +1,137 @@ - - - + + + - - incflo: An adaptive mesh, variable-density incompressible Navier Stokes solver - - - - - - - - - - - - - - - -
-
-
-

Getting Started

-
- -
    -

  • Clone

    - 
    -git clone https://github.com/AMReX-Codes/amrex.git
-git clone https://github.com/AMReX-Fluids/incflo.git
-
    -
    • + + Welcome to incflo’s documentation! — incflo 24.04-dev documentation + + + -

  • Setup Your Environment

    - 
    -export AMREX_HOME=/path/to/AMReX
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  • Visualize

    - AMReX output is supported natively by - yt, - VisIt, - Amrvis, - and ParaView. -
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Welcome to incflo’s documentation!

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incflo is an AMReX-based simulation code for modeling +the variable density incompressible Navier-Stokes equations in the presence +of complex geometries. It includes adaptive mesh refinement (AMR) +but without subcycling in time.

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For an AMReX-based incompressible flow code with subcycling in time, please see IAMR

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Active development in incflo is ongoing in the development branch.

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+

Contents:

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+ + - - + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 00000000..f1f69232 Binary files /dev/null and b/objects.inv differ diff --git a/search.html b/search.html new file mode 100644 index 00000000..0b688c1e --- /dev/null +++ b/search.html @@ -0,0 +1,132 @@ + + + + + + Search — incflo 24.04-dev documentation + + + + + + + + + + + + + + + + + + + + + +
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  • Search
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© Copyright 2017-2018, Incflo Team.

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+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+
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+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 00000000..e9b56ade --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["Debugging", "EB", "FluidEquations", "Fluids_Chapter", "GettingStarted", "InputsAlgorithm", "InputsCheckpoint", "InputsInitialization", "InputsLoadBalancing", "InputsMultigrid", "InputsPlotFiles", "InputsProblemDefinition", "InputsTimeStepping", "InputsVerbosity", "Inputs_Chapter", "Introduction", "ManagingGridHierarchy_Chapter", "TimeStep", "index"], "filenames": ["Debugging.rst", "EB.rst", "FluidEquations.rst", "Fluids_Chapter.rst", "GettingStarted.rst", "InputsAlgorithm.rst", "InputsCheckpoint.rst", "InputsInitialization.rst", "InputsLoadBalancing.rst", "InputsMultigrid.rst", "InputsPlotFiles.rst", "InputsProblemDefinition.rst", "InputsTimeStepping.rst", "InputsVerbosity.rst", "Inputs_Chapter.rst", "Introduction.rst", "ManagingGridHierarchy_Chapter.rst", "TimeStep.rst", 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