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8. Grid Unit
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flash4_ug
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7.1 Driver Routines
Contents
Index
IV
. Infrastructure Units
Subsections
8
. Grid Unit
8
.
1
Overview
8
.
2
GridMain
Data Structures
8
.
3
Computational Domain
8
.
4
Boundary Conditions
8
.
4
.
1
Boundary Condition Types
8
.
4
.
2
Boundary Conditions at Obstacles
8
.
4
.
3
Implementing Boundary Conditions
8
.
4
.
3
.
1
Additional Concerns with
PARAMESH
4
8
.
5
Uniform Grid
8
.
5
.
1
FIXEDBLOCKSIZE Mode
8
.
5
.
2
NONFIXEDBLOCKSIZE mode
8
.
6
Adaptive Mesh Refinement (AMR) Grid with Paramesh
8
.
6
.
1
Additional Data Structures
8
.
6
.
2
Grid Interpolation
8
.
6
.
2
.
1
Interpolation for mass-specific solution variables
8
.
6
.
3
Refinement
8
.
6
.
3
.
1
Refinement Criteria
8
.
6
.
3
.
2
Refinement Processing
8
.
6
.
3
.
3
Specialized Refinement Routines
8
.
7
Chombo
8
.
7
.
1
Using Chombo in a UG configuration
8
.
7
.
2
Using Chombo in an AMR configuration
8
.
8
GridMain Usage
8
.
9
GridParticles
8
.
9
.
1
GridParticlesMove
8
.
9
.
1
.
1
Directional Move
8
.
9
.
1
.
2
Point To Point Algorithm
8
.
9
.
1
.
3
Sieve Algorithm
8
.
9
.
2
GridParticlesMapToMesh
8
.
9
.
2
.
1
Uniform Grid
8
.
9
.
2
.
2
Paramesh Grid
8
.
10
GridSolvers
8
.
10
.
1
Pfft
8
.
10
.
1
.
1
Using
Pfft
8
.
10
.
1
.
2
Pfft
data movement subroutines
8
.
10
.
1
.
3
Unit Test
8
.
10
.
2
Poisson equation
8
.
10
.
2
.
1
Multipole Poisson solver (original version)
8
.
10
.
2
.
2
Multipole Poisson solver (improved version)
8
.
10
.
2
.
3
Multipole Poisson solver unit test (MacLaurin spheroid)
8
.
10
.
2
.
4
Tree Poisson Solver
8
.
10
.
2
.
5
Tree Poisson solver unit test
8
.
10
.
2
.
6
Multigrid Poisson solver
8
.
10
.
2
.
7
The direct solver
8
.
10
.
2
.
8
A Hybrid Poisson Solver: Interfacing PFFT with Multigrid
8
.
10
.
3
Using the Poisson solvers
8
.
10
.
3
.
1
Multipole (original version)
8
.
10
.
3
.
2
Multipole (improved version)
8
.
10
.
3
.
3
Tree Poisson solver
8
.
10
.
3
.
4
Multigrid
8
.
10
.
3
.
5
Hybrid (Multigrid with PFFT)
8
.
10
.
4
HYPRE
8
.
10
.
4
.
1
HYPRE Solvers
8
.
10
.
4
.
2
Unified Hypre Solver
8
.
10
.
4
.
3
Curvilinear Coordinates
8
.
11
Grid Geometry
8
.
11
.
1
Understanding 1D, 2D, Curvilinear
8
.
11
.
1
.
1
Extensive Quantities in Reduced Dimensionality
8
.
11
.
2
Choosing a Geometry
8
.
11
.
3
Geometry Information in Code
8
.
11
.
4
Available Geometries
8
.
11
.
4
.
1
Cartesian geometry
8
.
11
.
4
.
2
Cylindrical geometry
8
.
11
.
4
.
3
Spherical geometry
8
.
11
.
4
.
4
Polar geometry
8
.
11
.
5
Conservative Prolongation/Restriction on Non-Cartesian Grids
8
.
11
.
5
.
1
Prolongation
8
.
11
.
5
.
2
Restriction
8
.
12
Unit Test
9
. IO Unit
9
.
1
IO Implementations
9
.
2
Output Files
9
.
2
.
1
Checkpoint files - Restarting a Simulation
9
.
2
.
2
Plotfiles
9
.
2
.
3
Particle files
9
.
2
.
4
Integrated Grid Quantities - flash.dat
9
.
2
.
5
General Runtime Parameters
9
.
3
Restarts and Runtime Parameters
9
.
4
Output Scalars
9
.
5
Output User-defined Arrays
9
.
6
Output Scratch Variables
9
.
7
Face-Centered Data
9
.
8
Output Filenames
9
.
9
Output Formats
9
.
9
.
1
HDF5
9
.
9
.
1
.
1
Collective Mode
9
.
9
.
1
.
2
Machine Compatibility
9
.
9
.
1
.
3
HDF5 Data Format
9
.
9
.
1
.
4
Split File IO
9
.
9
.
2
Parallel-NetCDF
9
.
9
.
3
Direct IO
9
.
9
.
4
Output Side Effects
9
.
10
Working with Output Files
9
.
11
Unit Test
9
.
12
Chombo
9
.
13
Derived data type I/O
10
. Runtime Parameters Unit
10
.
1
Defining Runtime Parameters
10
.
2
Identifying Valid Runtime Parameters
10
.
3
Routine Descriptions
10
.
4
Example Usage
11
. Multispecies Unit
11
.
1
Defining Species
11
.
2
Initializing Species Information in
Simulation_initSpecies
11
.
3
Specifying Constituent Elements of a Species
11
.
4
Alternative Method for Defining Species
11
.
5
Routine Descriptions
11
.
6
Example Usage
11
.
7
Unit Test
12
. Physical Constants Unit
12
.
1
Available Constants and Units
12
.
2
Applicable Runtime Parameters
12
.
3
Routine Descriptions
12
.
4
Unit Test
13
. Cpp & Python units
13
.
1
Cpp
13
.
2
Python
13
.
2
.
1
Setup Generated Files
