Makeflo User`s Guide - Parallel Programming Laboratory
Contents
1. mesh msh or RocfloMP grda or grdb formats as described in Section 3 For RocfloMP the Makeflo command line to split a Gridgen input mesh named labScale grd boundary location file labScale inp and boundary def inition file labScale bcmp into 256 pieces writing the RocfloMP topology file Is top and RocfloMP mesh file ls grda the command line would be gt makeflo labScale grd 256 1s top 1ls grda For Rocflo to split the same Gridgen input mesh named labScale grd boundary location file labScale inp and boundary definition file labScale bc into 256 pieces writing the Rocflo topology file ls flo and Rocflo mesh files Is_001 msh through Is_256 msh the command line would be gt makeflo labScale grd 256 1s flo 1s_001 msh 2 1 Mesh Block File Names The standard CSAR pattern for block file names is prefix NNN ext Where prefix is a string identifying the run for example labScale NNN is the zero padded number of the block for example 001 and ezt describes the mesh format for example hdf Makef1lo always expects to be given the first block in the series for example labScale_0001 hdf the remaining block names are determined automatically When splitting a mesh into a thousand or more blocks you must should the 4 digit form 0001 when splitting into less than a thousand you should use the 3 digit form 001 Makeflo2. itself places no restriction on the number of digits 0000001 and 1 are completely acceptable 3 Mesh Formats Makeflo can read and write meshes in several formats The input and output formats are determined by the filename extensions on the input and output files The input and output formats need not be the same 3 1 Gridgen Mesh Format Makeflo can read but not write meshes in the Gridgen grd format To create such a mesh select a model in Gridgen choose Export Mesh select Ascii and Double Precision and specify a filename This is the most common mesh input format used by Makeflo Unlike the other formats all the blocks in a mesh go into a single file with this format As such no special numbering conventions are needed or used but the file must have the appropriate extension Use grd for files written using ASCII mode grds for files written using binary single precision mode and grdd for files written using binary double precision mode Note that Gridgen s binary output files are not compatible across machine architectures but binary files are substantially smaller than ASCII files In Gridgen to output a grd file from the top level menu choose Input Output e gt Grid Pts Export 8 gt Block Volumes 4 gt Name k gt type in name ending with grd grds or grdd gt For grd format ascii a precision double d For grds form
3. 000001 hdf will work nicely 3 3 Rocflo Mesh Format Makeflo can read or write meshes to Rocflo s native binary format which con sists of the following fields written to a Fortran unformatted binary data file time ni nj nk x i j k yGi j kK 2 i j k i 1 ni j 1 nj k 1 nk Where time and the x y and z arrays are all double precision floating point numbers in the local machine s native format and ni nj and nk are all integers in the machine s native format As such Rocflo mesh files generated on one machine will not work on another machine with a different architecture The file extension for this format is msh Like HDF each block of the mesh comes in its own file and you provide the filename of the first block 3 4 RocfloMP Mesh Format Makeflo can write but not read meshes to RocfloMP s native binary format which consists of the following fields written to a Fortran unformatted data file time for each block block ni 1 nj 1 nk 1 C x i j k i 1 ni j 1 nj k 1 nk C y i j k i 1 ni j 1 nj k 1 nk C z i j k i 1 ni j 1 nj k 1 nk The grda version is ASCII formatted the grdb version is Fortran un formatted binary In both cases the entire mesh is written to a single file 4 Boundary Condition Formats Makeflo automatically determines and inserts internal boundary conditions which form the boundaries between blocks of a mesh External boundary condi tion
4. Makeflo User s Guide Center for Simulation of Advanced Rockets March 18 2004 1 Introduction 1 1 Goal and Scope The goal of this guide is to allow users to create input files for the structured grids fluid dynamics solvers in the Center for Simulation of Advanced Rockets coupled physical simulation code This document describes Makeflo a small command line utility program used to create structured grids input files This document describes the inputs required by Makeflo the purpose and results of Makeflo and the outputs produced 1 2 Related Documents e Makeflo Developer s Guide e RocfloMP User s Guide e Rocflo User s Guide e Gridgen tm User s Manual http www pointwise com 1 3 Summary Makeflo reads a serial mesh for example as generated by Gridgen splits the mesh into a user specified number of pieces and writes out the resulting mesh pieces and a topology file describing how the pieces fit together The mesh pieces and topology files can then be passed to a structured grids solver such as Rocflo Makeflo is a necessary step in any structured grids rocket simulation run IGridgen is a commercial gridding product by Pointwise Inc which is not in any way affiliated with CSAR or the University of Illinois Input Serial Mesh Split Mesh i Makeflo Rocflo External All Boundary Boundary Conditions Conditions Figure 1 Rocflo input files and proce
5. at binary b precision single s For grdd format binary b precision double d style PLOT3D 2 Done ent gt Pick All a Done ent The format of this file is the same for ASCII or binary versions and consists of the number of blocks in the mesh the i j k dimensions of each block for example 8 15 17 then the coordinates of the nodes of each block in C exponential notation for example 3 456e 01 The x y and z coordinates are in the unusual order do b 1 nBlocks C x i j k i l ni b j 1 nj b k 1 nk b CCy i j k i 1 ni b j 1 nj b k 1 nk b Figure 4 Grid Points Export dialog box in Gridgen C z i j k i 1 ni b j 1 nj b k 1 nk b end do 3 2 HDF Mesh Format Makeflo can read or write meshes in the HDF4 Single File Scientific Data Set DFSD API format This format is binary double precision and platform independent Note that these files do not write the CSAR hdf block header and hence are not yet readable by Rocketeer The file extension for this format is hdf Each block is contained in a separate file with the numeric part of the filename indicating the block number You always provide the filename of the first block and must provide enough zeros in the filename for the largest block for example when writing 5000 blocks a filename like out01 hdf does not have enough zeros and will fail but out00001 hdf or out
6. at Urbana Champaign HEAHHHEAHHHAA EH HAA AHHH RHHRAR HHA AHH RA RHEE HH Gridgen type 2 solid surface map to slip wall 2 60 0 HHHHHHHHREHHHEHHHHHHEAAAEAA RARER RAH RRR Gridgen type 5 inflow This is an ignition boundary a burning surface 5 10 1 HHHHHHHHE AHHH HHHHHHRAAAHHAR AHHH HHH R RRR ARR Gridgen type 6 outflow This is a supersonic subsonic exit 6 20 0 HEHHEHHHHEHHAHHHEH HEH HEHEHE HEHHEHRE HHH HEHEHE HEHE Unspecified condition default 0 999 0 HEHHHHRAHHHAAEHHAEAHHEAREREER RARER ERE A REHEARSE Gridgen type 8 generic 1 Currently used to model fuel face at head end Change these BC to be whatever type is desired to either allow burning or inhibit this fuel surface 8 10 1 5 2 Sample Rocflo bc file Boundary condition types for fluid dynamics Center for Simulation of Advanced Rockets University of Illinois at Urbana Champaign HHEAHHHAAHHHAA AHHH RHHRAR HHA E RHEE A RRA Raa These are the initial conditions of the fluid 1 5 100000 293 0 0 0 number of vars initial pressure temp velocities tets 1e Tie Reynolds number and reference values 1115 Diagnostics to write out each step 11 000 Adaptive mesh control disabled HHEHHHHEAHHHAA HH HAE AHHH RHHHAR HRA A HHH RA RAS Gridgen type 2 solid surface 2 16 HHHHHHHHRRRHHHHHHHHAAAAHHA RAE HHHR RRR R ARR Gridgen type 5 inflow This is an ignition boundary a burning
7. ck The second line gives the block name as a human readable ASCII string The third line gives the number of distinct boundary conditions applied over the block typically 6 one per face but can be as large as desired Makeflo fully supports sub block boundary conditions Each boundary condition begins with a line that gives the 1 based i j and k spans covered by the condition and then a boundary condition number For example a number 5 boundary condition over the large i face of a 8x11x17 block would be described by the line 8 8 1 11 1 17 5 A number 1 boundary condition describes an internal boundary and is followed by an extra line which Makeflo ignores All other boundary condition numbers are described by a single line See Section 5 3 for an example boundary location file 4 2 RocfloMP Boundary Definition bcmp A RocfloMP boundary definition file maps Gridgen boundary condition numbers to RocfloMP boundary condition numbers The boundary definition file has extension bcmp and is typically written manually by the user This is a line oriented ASCII text file The file consists of a sequence of definitions each of which fits on a single line For example the line 5 10 1 Lists the mapping between e The input file boundary condition number here 5 for a Gridgen inflow e The output RocfluMP boundary condition number here 10 for a RocfloMP burning surface e Flag indicating this boundary type should participat
8. e in mesh motion here 1 for a moving boundary Any line starting with is a comment and hence ignored See Section 5 1 for a complete RocfloMP boundary definition file The RocfloMP boundary definition file and the Rocflo boundary definition file described below have different formats This is because the RocfloMP top file requires different information from the Rocflo flo file 4 3 Rocflo Boundary Definition bc A Rocflo boundary definition file maps Gridgen boundary condition numbers to Rocflo boundary condition types and parameters The boundary definition file has extension bc and is typically written manually by the user This is a line oriented ASCII text file The file consists of a sequence of definitions each of which describes a single boundary condition number An character begins a new definition and is followed by the Gridgen boundary number to be described For example the definition for Gridgen boundary condition number 8 would begin with a line containing 8 The remainder of a definition consists of plain text that is copied directly into the flo file except for the character and the character A character is replaced in the flo file by the coordinates of the location of the boundary condition in the current block A character at the start of a line begins a comment line which is ignored The character is special only at the start of a line Empty lin
9. es are also ignored Each block begins with the definition of the special number 1 which defines the fluid initial conditions and which must be present Boundaries for which no external boundary condition is specified for example because no inp input file was available are given boundary number 0 by default These numbers and any other boundary number referenced in the inp file must all be defined in the boundary definition file 4 3 1 Example Rocflo Boundary Definition A typical section in the boundary definition file then is Gridgen boundary number 8 generic 1 Models the fuel face at the head end 8 119 Ignition boundary 2855 FIXGRD IGNITION NO_TURB_WALL 119 is the Rocflo boundary condition number the gets replaced with the location of the boundary and the remaining lines are parameters for the boundary condition See the Rocflo user s manual for a detailed description of the acceptable boundary condition numbers and their parameters The above definition would expand to the following text if a number 8 bound ary was encountered on the small 7 face of an 8x12x16 block 119 1 1 1 12 1 16 Ignition boundary 2855 FIXGRD IGNITION NO_TURB_WALL See Section 5 2 for a complete Rocflo boundary definition file 10 5 Sample Files 5 1 Sample RocfloMP bcmp file RocfloMP boundary condition types for fluid dynamics Center for Simulation of Advanced Rockets University of Illinois
10. nal multilevel flag To use RocfloMP s multi level multigrid solver pass multilevel m where m is a positive integer at least 1 that gives the number of separate smaller grids to create By default there is only one grid which can have any size For example multilevel 2 creates another smaller grid of half the size on each axis and requires each input block to have an even number of cells along each axis In general multigrid level m requires all input blocks to have a multiple of 2 cells and will restrict Makeflo to only cutting along 2 cell boundaries 4 The first input mesh file The input mesh can be in either HDF hdf Rocflo mesh msh or Gridgen grd formats as described in Section 3 The external boundary condition location inp and boundary condition definition bc or bcmp files must have the same base name as the mesh file 5 The number of blocks in the output mesh This is typically at least the number of processors but may be larger If there are already at least this number of blocks in the input mesh no splitting is performed 6 The topology file name To select Rocflo output this filename should end with flo for RocfloMP output it should end with top The standard CSAR pattern for topology file names is prefiz flo or pre fiz top where prefiz is a string identifying the mesh 7 The first output mesh file The output mesh can be in HDF hdf Rocflo
11. s such as the location of the ignition boundary reflection walls and outflow boundaries must be specified by the user The external boundary conditions are described in two steps first a bound ary location file maps block locations to boundary condition numbers then a boundary definition file maps boundary condition numbers into a Rocflo or RocfloMP boundary condition type and parameters Both the boundary location and boundary definition files are found by re placing the extension of the first input file with the corresponding extension For example if the input block file is test001 hdf the boundary location file must be named test001 inp and the boundary definition file must be named test001 bcmp RocfloMP or test001 bc Rocflo Because Rocflo or RocfloMP handle boundary conditions differently the boundary definition file has a different extension and format for each solver as described below 4 1 Boundary Locations The only supported format for boundary locations is Gridgen inp format To export this format from Gridgen choose Boundary Conditions then Export Database The inp format is line oriented ASCII The first line is the Gridgen solver number always 1 for the generic solver The second line gives the number of blocks in the mesh The remainder of the file consists of descriptions for each block The first line of a block description gives the i j k dimensions of the blo
12. split along the longest axis which produces much better results 2 Optional splitrcb flag By default makeflo shifts partition boundaries to ensure the best possible load balance For example in cutting a 2 block Since several blocks can co exist on a processor a 16 block mesh may be used with fewer processors input mesh into 9 output blocks if makeflo allocates 5 output blocks to the left input and 4 output blocks to the right input the resulting mesh is as shown in Figure 2 Figure 2 The default partitioning method optimizes for load balance Note how the left input block is split into 5 equal sized pieces However note that the boundary between the left and right input blocks is offset slightly which can increase the number of messages sent between the left and right halves If this communication cost is more important than load imbalance it may be preferable to divide the blocks in a more conformal manner The splitrcb flag forces blocks to be recursively split down their centers as illustrated in Figure 3 Figure 3 splitrcb optimizes for communication Note that now the left and right block boundaries line up which should minimize the number of messages sent However note that this mesh is not as well load balanced as the mesh of Figure 2 In general meshes generated with splitrcb will be less well balanced than meshes generated normally but will have slightly better communication Optio
13. ssing stages 1 4 Motivation Rocflo requires the problem domain to be described as a set of blocks Each block is a regular rectangular array of elements or cells Together the set of blocks is called a mesh In parallel Rocflo assigns each block to exactly one processor that is blocks are indivisible units of computation This means that a mesh with 16 blocks cannot use more than 16 processors of a parallel machine To use more than 16 processors the blocks must be split into smaller blocks before running Rocflo Makeflo performs this splitting In addition each block requires boundary conditions both internal bound aries which describe how block fit together as well as external boundaries be tween the fluid domain and the outside world Makeflo computes the internal boundary conditions and also splits the user specified external boundary con ditions as it splits blocks These boundary conditions are written to a Rocflo topology file Together the splitting and boundary condition generation form a pre processing step that prepares a mesh for use by Rocflo The overall processing flow is shown in Figure 1 2 Command Line Usage Makeflo is a command line utility The command line parameters are 1 Optional splitaxis flag If you prefer to split the blocks only along a particular axis specify the axis with splitaxis a where a is 0 for the i axis 1 for the j axis and 2 for the k axis The default is to recursively
14. surface 5 119 Ignition boundary 2855 FIXGRD NO_IGNITION NO_TURB_WALL HHHHHHHHREHHHHHHHHHRAAAHAA ARERR REAR RRR Gridgen type 6 outflow This is a supersonic subsonic exit 6 25 Supersonic subsonic exit 100000 HHEHHHHHHEHHHHHHHHHHEEHHEHHHHEEHHEEHRHREEHRAH RHEE The user is expected to go in later and fix these unspecified conditions using the fix_bc sh script HHEHHHHHHEHHEHEHHHHHHEEHEHRHHHRAEHHEHHRHREE REE HAE Unspecified condition default O bc_unspecified External BC bc_unspecified_desc bc_unspecified_params 12 5 3 Sample inp file 1 141 17 17 17 24 17 17 17 17 17 26 17 17 17 17 17 17 17 17 117 15 15 17 17 25 17 17 17 27 S17 17 17 15 BA 17 17 17 17 17 15 15 17 17 17 17 17 136 15 15 15 15 15 15 17 17 17 17 17 15 15 FD 15 15 15 15 15 15 15 15 15 15 15 17 132 17 17 17 130 17 17 17 17 17 17 129 15 15 15 15 15 15 15 125 15 15 15 15 file continues 13
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