AGRIF Adaptive Grid Refinement In Fortran User's Guide Version 1.3
Contents
1. This means that the type of the variable the indices of the first point in the domain and the type of its dimensions must be declared We should call following subroutines T e Position of the variable 1 Description We should specify the position of the variable on the grid by calling the subroutine Agrif_Set_type That allows the use of staggered grids For each space direction we use 1 for the boarder of a cell figure 1 1 and 2 for the center of the cell figure 1 2 Remember that a staggered grid variable can be used in a space direction only if this direction is refined e e e e Figure 1 1 Positions of a grid variable on a no staggered variable re e e e Figure 1 2 Positions of a grid variable on a staggered variable Next it is necessary to declare the index of the first point of the variable which is inside the computational domain At last the user must indicate the type of each dimension by using the subroutine Agrif_Set_raf x y or z for a space dimension 0 for a no space dimension 2 Syntax Call Agrif_Set_type u p1 p2 i1 i2 pl p2 p3 i1 i2 i3 integ Call Agrif_Set_raf ur nl77n2 7 nl n2 n3 x y z or N p1 p2 p3 indicate the position of the grid variable and i1 i2 i3 the index of the first point in the domain 3 Example For a 2D domain four different ways for positionning a variable on a cell are possible Call Agrif Set type vr 1 1 1 1 Call Agrif2. eee 12 Special Operations Ua ES bt etek ae du og 12 1 4 1 Special values with interpolations 12 1 42 Getting the values on the parent grid 13 1 43 Using fixed grids in AGRIF 14 Using AGRIF in a multidimensional finite difference model 17 Necessary subroutines to run AGRIF 17 2 1 1 Subroutines provided by AGRIF 17 2 1 2 Subroutines to be written by the user 17 How to compile AGRIF and your model with AGRIF 18 2 2 1 Changes in the Makefile 18 2 2 2 Changes in the model sion 4 44 4 4 data au 19 2 2 3 How to use the AGRIF package 20 Chapter 1 Description of AGRIF To use AGRIF the user needs e to write a configuration file which contains model s description This file is read by the CONV during the code compilation e A file where fixed grids are defined e The file agrif_user F90 which contains users subroutines e The file agrif2model F90 which make the link between the model and the agrif library this file should not be modify All those steps are detailed below 1 1 The configuration file The syntax used in the configuration file is presented next All examples given here have no real signification practicals examples are presented in the tutorial 1 1 1 Global parameters Refinement dimension and domain size 1 Description The refinement dimension and the domain size are set with
3. of cells and nxp1 the number of grid points then the sentence nxpi nx 1 must be written in this routine 17 Agrif_Initworkspace is called after each change of grid to recalculate the corresponding values Agrif_Detect This routine is necessary if AGRIF is used in adaptative mode It allows to write the adaptative mesh raffinement criterion 2 2 How to compile AGRIF and your model with AGRIF 2 2 1 Changes in the Makefile The Makefile should be modify in order to use AGRIF library Create a AGRIF key In order to determine if AGRIF is used or not in the current model we should created an AGRIF key Let s say key_agrif CCP_FGLAGS Dkey_agrif This key allows to e Compile or remove the AGRIF source code during the preprocessing For example in the source code if defined key_agrif code for AGRIF else code without agrif endif e Determine in the Makefile if AGRIF should be used ifneq findstring key_agrif CPPFLAGS Makefile with AGRIF else Makefile without AGRIF endif 18 Compile the AGRIF library The AGRIF directory should be place in code tree In the makefile we should begin with AGRIF library compilation in order to create a libagrif a file which could be used later To compile it the user should use the Makefile presents in AGRIF Use CONV Add the compilation of the file Agrif_User F90 at the end of the object list Now we should create a source code compatible with AGRIF us
4. refinement factors 1 Description The space refinement factors for new grids created by adaptive mesh refinement are set by subroutines Agrif_Set_coeffref_x Agrif Set_coeffref_y and Agrif_Set_coeffref_z 2 Syntax Call Agrif Set coeffref x 3 n integer Call Agrif_Set_coef e Time refinement factors 1 Description The time refinement factors for new grids created by adaptive mesh refinement are set by using subroutines Agrif Set _coeffreft x Agrif Set_coeffreft_y and Agrif_Set_coeffreft_z 2 Example Call Agrif_Set_coeffreft_x 2 Call Agrif_Set_coeffreft_y 2 Call Agrif_Set_coeffreft_z 2 Minimum width 1 Description The minimum width is the minimum size of the grids in number of cells created during the regridding operation This number is set with the subroutine Agrif Set minwidth 2 Example Call Agrif Set minwidth 5 e Maximum number of refinements 1 Description The maximum number of refinement is defined for all space direction by using subroutines Agrif Set_rafmax 2 Example Call Agrif_Set_rafmax 5 1 2 2 Agrif Init Values subroutine This subroutine is called once on each fine grid Firstly we should call the subroutine which allows to initialize the cur rent grid the same subroutine which allows to initialized the coarse grid Call init If some specific treatments of one variable are required initialization boundary interpolation restoration this one has to be fully declared
5. the key word nD followed by one two or three integer values corresponding to the number of cells in the directions of refinement Note that those integers must be global variables which must be de fined in the parameter file and probably declared as parameters in the original model 2 Syntax nD nt n2 n3 n 1 2 3 nl n2 n3 strings 3 Examples 3D nx ny nz 3D refinement 2D nx ny 2D refinement the model can be 2D or 3D Parameter file 1 Description The parameter file is the usual model s file in which several param eters are declared as the indexes delimiting the domain for example Actually the essential condition is that this file must contain the dec laration of the cells number If it is an included file its name is given after the keyword paramfile If these variables are defined in a module we should use the keyword parammodule 2 Syntax paramfile name name string of characters parammodule name name string of characters 3 Example paramfile parameter h parammodule modulename Using fixed grids 1 Description Keyword FIXED_GRIDS indicates that some fixed grids are used 2 Syntax USE FIXED_GRIDS 3 Example USE FIXED_GRIDS Using only fixed grids 1 Description Keyword ONLY_FIXED_GRIDS indicates that only some fixed grids are used without moving grids They are defined in the Agrif_Fixedgrids in Syntax USE ONLY_FIXED_GRIDS Exampl
6. AGRIF Adaptive Grid Refinement In Fortran User s Guide Version 1 3 27 novembre 2006 AGRIF is a package for the integration of adaptive mesh refinement AMR features within a multidimensional model written in Fortran and discretized on a structured grid The package mainly consists in two parts It first provides model independent Fortran 90 procedures implementing the usual parts of an AMR process like time integration algorithm of the grid hierarchy clustering algorithm re finement algorithm interpolation and update procedures In a second part the Fortran model dependent code is created via a program which analyses a user s written configuration file The model independent part is compiled alone The model dependent part is then compiled with the current model Then they are linked The first chapter deals with files which could be write in order to use AGRIF The second one is based on the current model modification and also the way to use to compile the model and AGRIF Contents 1 Description of AGRIF 2 1 1 1 2 1 3 1 4 2 1 2 2 3 The configuration file te Ga Ne MS AE LR dE Sas Bed 3 1 1 1 Global parameters He din dk ELA Ras a are 3 LOU fle e ga a re DA de A re 5 1 2 1 Agrif Init Workspace subroutine 6 1 2 2 Agrif InitValues subroutine 7 1 1 2 3 Agrif detect subroutine Glee a oh ape Du 1 Agrif Model file 6 bad ales Goda Ae ho Be dhe dk Pas
7. Set type u 2 1 1 1 Call Agrif Set type v 1 2 1 1 Call Agrif Set type h 2 2 1 1 Call Agrif Set Raf u y N Figure 1 3 shows these positions on a cell 8 O O O O ES Rr rahe a UE ET ES SRE RESTES LR PTE ER ERP Seat d eE ene at gt a a e A E E N O Oo o u 1 1 lt oS gt 8 8 vi Oo 0 oO O 0 vr 1 1 v 1 1 Figure 1 3 First points in the domain e Interpolation 1 Description AGRIF can interpolate variables of the current grid which are declared with the subroutine Agrif_Set_interp in this subroutine 2 Syntax Call Agrif_Set_interp name interp method method of interpolatior 3 Example Call Agrif_Set_interp u interp Agrif_linear e Boundary interpolation 1 Description AGRIF can in a similar way provide subroutines for the interpolation of boundary values if necessary The name of the concerned variables must be given after with the subrou tine Agrif Set_bc followed by a description such as ideb ifin or iind where these last indices indicate where to interpolate For variables which have been also declared by with the subrou tine Agrif Set_interp the default interpolation type used in the boundary corrections is the same that the one used in the Agrif Set_interp called If the variable is not declared by using the subroutine Agrif Set_interp or if another kind of interpolation for the boundary is desired the subroutine Agrif_Set_bcinterp s
8. ble a point on a parent grid always corresponds with a point on the child grid whatever the space refinement factors are the same holds for a staggered variable with an odd space refinement factor Concerning a staggered variable with an even space refinement factor this correspondence does not exist as it is shown on the figure 1 7 Points of the fine grid iS eee Point of the coarse grid N e AA i e i K val Coarse cell Fine cells Figure 1 7 Staggered variable with a space refinement factor equal to 2 The correspondances between the fine and coarsed grids points are given by the following algorithm Do i ideb coef fraf Varg ideb 5 Var i End Do where the values of ideb and ideb depend on the type of the variable staggered or no staggered ite ie No staggered variable ix ptx 1 Staggered variable ix ptx 1 where ptx is the index of the first point inside the domain and ix the minimum position of the current grid on its parent grid 1 4 3 Using fixed grids in AGRIF One of the features of the AGRIF package is its ability to deal with the use of fixed fine grids in the domain 14 First the user must insert the keyword USE FIXED_GRIDS in the config uration file he must add the keyword USE ONLY_FIXED_GRIDS if he want to use only fixed grids and no moving grids Next he must declared the fine grids in a file called AGRIF_FixedGrids in which has to be in the
9. current directory where the code runs For each fine grid and each space direction a line indicates its position on its parent grid and its space and time refinement factors Syntax e ID imin imax spacerefx timerefx e 2D imin imax jmin jmax spacerefx spacerefy timerefx timerefy e 3D imin imax jmin jmax kmin kmax spacerefx spacerefy spcerefz timerefy timerefz Imin imax jmin jmax kmin kmax are six integers indicating the minimum and maximum positions of the fixed grids in this definition the positions of the corner points refer to the positions of the parent grid corners starting with the value 1 in each space direction When the user writes these positions he has to take care that each fine grid is contained in a parent fixed grid Spacerefx spacerefy spcerefz timerefx timerefy and timerefz are six integers indicating space and time refinement factors in the x y and z direc tions If one of these factors are equal to 1 it means there is no refinement in the concerned space direction Example Figure 1 8 gives an example in dimension 2 The root coarse grid Go has two child grids G and Gy and Gi has one child grid G3 Space and 15 timerefx time refinement factors are equal to 2 in both space directions Figure 1 8 Fixed grids example For this example the AGRIF_FixedGrids in file must contain the follow ing lines GO has 2 child grids G1 and G2 T 4 T 2 2 2 2 posi
10. e USE ONLY_FIXED_GRIDS not grid dependent variables 1 1 2 Description Keyword notgriddep indicates that a variable is not grid dependent Consequently these variable value will be the same on each grids and will not stored in the table tabvars Syntax notgriddep name name string of characters Example notgriddep variable_name agrif_user file Severals subroutines should be defined in this file e Agrif_Init Workspace e Agrif_Init Values e Agrif_detect Those subroutines are defined below 1 2 1 Agrif Init Workspace subroutine In this subroutine the user should define all variables which are computed from the grid dimension on the fine grid For example if NOT Agrif_Root then nxi nx 1 nyi ny 1i endif If the amr has been defined in the configuration file all AMR parameters should be defined in this subroutine e Efficiency 1 Description The efficiency is relative to the clustering algorithm and represents the proportion of grid points included in the newly created points which were really detected The default efficiency is set to 70 The user can change this value the subroutine Agrif Set Efficiency 2 Example Call Agrif Set Efficiency 0 8 e Regridding 1 Description The regridding operation is performed periodically ev ery N coarse grid time steps This number N is set by the subrou tine Agrif Set Regridding 2 Example Call Agrif Set Regridding 10 e Space
11. hould be called 2 Syntax Call Agrif Set bc var ideb ifin ideb ifin integers Call Agrif_Set_bcinterp var method method linear lagrange spl Figure 1 4 represents in 2D and for the different types of vari ables the positions which will be corrected if you specify 1 Figure 1 5 represents in 2D and for the different types of vari ables the positions which will be corrected if you specify 0 Figure 1 6 represents in 2D and for the different types of vari ables the positions which will be corrected if you specify 1 typex 2 typex 1 typey 1 typey 2 Figure 1 4 Grid corrections BC var 1 e Update of the grid variables The AGRIF package is able to update grid variables from their parent grid 1 Description AGRIF can update the variables of the parent grid of the current grid which are declared with the subroutine Agrif Set UpdateType 2 Syntax Call Agrif_Set_UpdateType var update method method of interpolat 3 Example 10 Call Agrif Set UpdateType u update Agrif Update Average e Restoration adaptive mesh refinement only 1 Description During a step of mesh refinement and for each variable the user can specify that its value must be restored if possible for the initialization of the newly created grids This is accomplished by calli
12. ing the CONV program Consequently for each file compilation e we should move this file in an other directory in order to work on the file without removing the original one e apply the conv on this file which allows to create a new fortran file e compile this new file For example let s use a directory call NEW_FILES Foe each file compila tion we should have CPP CPPFLAGS F90 gt NEW_FILES F90 cd NEW_FILES conv agrif in comdirin comdirout AGRIF_MODELFILES CPP CPPFLAGS INEW_FILE AGRIF_INC NEW_FILE AGRIF_MODELFILES F9 F_C NEW_FILE F90 Compile Agrif2Model file Just before the final link the user should complete the Agrif2Model file with the help of files presents in AGRIF_INC directory by preprocessing 2 2 2 Changes in the model This section describes the few changes the user has to make in his original code to be able to run the AGRIF package 19 Modifying the parameter file This file must contain the domain sizes and variables that depend on those sizes For example if you had in your original common a declaration like integer nx ny nz parameter nx 100 ny 100 nz 30 integer parameter nxpi nx 1 nypi ny i nzpi nz 1 change it into integer nx 100 ny 100 nz 30 integer nxpi nx 1 nypi ny 1 nzpi nz 1 Modifying the main program For running AGRIF you should replace the call to your original time inte gration procedure by call AGRIF_STEP see sectio
13. n 2 1 1 You should also add a call to the Agrif_Init_Grids see section 2 1 1 sub routine This call must be done after the initialization of the number of cells Writing some procedures You should write the Agrif_Initvalues and Agrif_Initworkspace procedures see section 2 1 2 2 2 3 How to use the AGRIF package After making the changes described in the previous section the user has to write the configuration file see section 1 1 and to compile the library Writing the AGRIF_FixedGrids in file This file described in section 1 4 3 is necessary if you want to use some fixed grids It must be positioned in the main directory where the model runs Writing the configuration file Here we try to present how the user could process to get an idea of what he should put in the configuration file 1 count the numbers of cells in the X Y and Z directions 20 2 get the parameter file name 21
14. ng the subroutine Agrif_set_restore 2 Syntax Call Agrif_set_restore var 3 Example Call Agrif_set_restore u Call Agrif_set_restore v 1 2 3 Agrif detect subroutine This subroutine is used in order to detect points where raffinement is re quired This subroutine should be write when an adaptative mesh raffinement is necessary 11 1 3 Agrif2Model file The CONV program allows to create a new fortran code and also files in AGRIF_INC directory which are used to complete the agrif2model file So in the Makefile we should compile the agrif2model file at the end of the compilation just after the compilation of the last model file 1 4 Special Operations 1 4 1 Special values with interpolations Before a call to the Agrif Interp_VarName or Agrif Bc_VarName subrou tines you can specify the use of some special values for the arrays of the parent and fine grids concerned by these interpolations The necessary keywords are Agrif UseSpecialValue and Agrif SpecialValue for the parent grids Agrif UseSpecialValueFineGrid and Agrif SpecialValueFineGr for the fine grids Agrif_UseSpecialValue and Agrif_UseSpecialValueFineGrid are two logicals whereas Agrif_ SpecialValue and Agrif Special ValueFineGrid are two reals Special values on the parent grids If you want to use a special value for the parent grid for example 98 8 here you must add the following line
15. s before any call to an Agrif_Interp_VarName 12 or Agrif_Bc_VarName subroutine AGRIF_UseSpecialValue TRUE AGRIF_SpecialValue 98 8 Then if a value on the part of the parent grid used for the space inter polation of the fine grid is equal to 98 8 this value will be replaced if possible by the nearest value of the parent grid different of 98 8 Special values on the fine grids If you want to use a special value for the fine grid for example 50 0 here you must add the following lines before any call to an Agrif_Interp_VarName or Agrif_Bc_VarName subroutine AGRIF_UseSpecialValueFineGrid TRUE AGRIF_SpecialValueFineGrid 50 0 Then if a value on the fine grid is equal to 50 0 this value won t be replaced during the interpolation 1 4 2 Getting the values on the parent grid Sometimes the user need to know the values on the parent grid of the cur rent grid to write its own routines of interpolation and update for example AGRIF offers this possibility How to get the values on the parent grid In order to get the value on the parent grid we should call the function Agrif Parent Example Agrif Parent u e For a scalar variable Real dtp dtp Agrif Parent dt e For a multidimensionnal variable Real Dimension pointer parent_u 13 parent u Agrif Parent u parent_u i j 3 What is the correspondance between points on fine and parent grids For a no staggered varia
16. tions and refinement factors fo T 1 3 2 2 2 2 positions and refinement factors fo Gi has 1 child grid G3 10 2 6 2 2 2 2 positions and refinement factors fo G3 has no child grid G2 has no child grid O BH ANNY Fixed grids with adaptive mesh refinement When the keyword USE FIXED_GRIDS is in the configuration file without the keyword USE ONLY_FIXED_GRIDS you have at the same time in the grid hierarchy fixed grids and moving grids 16 Chapter 2 Using AGRIF in a multidimensional finite difference model 2 1 Necessary subroutines to run AGRIF 2 1 1 Subroutines provided by AGRIF Agrif_Init_Grids This routine creates the characteristics of the root coaser grid number of cells It is called in the main file after the initialization of the number of cells on the coarser grid Agrif_Step This routine calls and replaces the user s time integration procedure named Step the user has to write It integrates the model forward on all grids and performs a regridding at regular interval in case of adaptive refinement 2 1 2 Subroutines to be written by the user Agrif_Initvalues This routine allows to initialize the fine grid variables It is called in the procedure of refinement Agrif Initworkspace This routine contains for each space direction the links between variables declared in the parameter file and representing the size of the domain and the number of cells For example if nx is the number
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