Home

User Manual Version 1.1 - Computational Infrastructure for

1. a es a e O e e a EE TEN EE wt oak sel Seal T a 654 Install s ti eS ns Se eS ee Hee Ree Ee Eee EERE 6 6 Install without using configure o e e 6 7 Install using cmake 2 4s Bi ede e ee ee eee eee eee Ge 7 Simulation procedure 24 8 Examples 26 8 1 Examples for preprocessing program 00 26 8 2 Examples of dynamo benchmark o o 28 ek en ee ne en RA So 29 8 4 Example of heat and compositional source LL 2 aa vrake avs 29 29 9 Preprocessing program gen_sph_grid 30 9 1 Position of radial grid o o e keen 30 9 2 Control file control_ sph shell l oooo ooooo 44 4 mm 31 A E en 32 9 4 Finite element mesh data ee 33 DE EE ek eT ae ee nd ee E E 33 10 Simulation program sph_mhd 34 10 1 Control file a ee ee EER SRSA ERE OLE ORE HEH 36 10 2 Spectrum data for restarting 2 2 arr kr vnr rane 39 denne 39 EDEN ENDENE NEED 40 10 4 1 Distributed VTK datal o av 40 EE ee an en en dn E 42 By oe ee NE 43 od ee eee ee ee E 44 NT 45 EEE EE EE nn ee 45 Pat ad pe gua glee ales aoe pees 46 10 6 Gauss coefficient data gauss_coef_prefix dat 48 10 7 Spectrum monitor data picked sph prefix dat 48 1 Data transform program sph_snapshot and sph_zm_snapshot un 2 Initial field generation program sph initial field 52 3 Initial field modification program
2. temperature TEMPERATURE Temperature for reference temperature is defined by real A9 time step_ctl Time stepping parameters are defined in this block Back to control MHI D Back to control_assemble_sph elapsed time ctl ELAPSED_TIME Elapsed wall clock time second for simulation ELAPSED TIME is defined by real This parameter varies if end step ISTEP_FINISH is defined to 1 If simulation runs for given time program output spectrum data rst_prefix elaps process fst immediately and finish the simulation i_step_init_ctl ISTEP_START Start step of simulation ISTEP_START is defined by integer if ISTEP_START is set to 1 and IN I AL_TYPE is setto start_from rst_file program read spectrum data file rst_prefix elaps process fst and start the simu lation i_step_finish_ct ISTEP_FINISH End step of simulation ISTEP_FINISH is defined by integer If this value is set to 1 simulation stops when elapsed time reaches to ELAPSED_TIME i_step_check_ctl ISTEP MONITOR Increment of time step for monitoring data ISTEP MONITOR is defined by integer isteprstctl STEP RESTART Increment of time step to output spectrum data for restarting ISTEP RESTART is defined by integer
3. end num grid sph end spherical shell ctl Figure 3 Example of Control file 27 with inner core Example to generate indexing data including inner core and exter nal of the fluid shell 8 2 Examples of dynamo benchmark There are four examples for simulations using dynamo benchmark test as following Case 0 Example of dynamo benchmark case 0 Thermally driven convection without magnetic field Case _1 Example of dynamo benchmark case 1 Dynamo model with co rotating and electrically insulated inner core Case_2 Example of dynamo benchmark case 2 Dynamo model with rotatable and con ductive inner core Compositional case 1 Example of dynamo benchmark case I using compositional variation instead of temperature The process of the simulation is as following 1 Change to the directory for Benchmark Case 1 for example username cd CALYPSO_DIR examples dynamo_benchmark dynamobench_casel 2 Create the grid files for the simulation dynamobench_case_1 CALYPSO_DIR bin gen_sph_grids 3 Run simulation program dynamobench_case_1 mpirun np 4 CALYPSO_DIR bin sph_mhd 4 To continue the simulation change the parameter rst ctl in control_MHD from dynamo_benchmark_1 to start_from_rst_file and continue sim ulation by repeating step 2 5 To check the results for dynamo benchmark run dynamobench_case_1 mpirun np 4 CALYPSO_DIR bin sph_dynamobench 28 8 3 Example of data assembling
4. Inner Core Outer Core Conductive fluid Conductive solid or insulator Insulator Figure 1 Rotating spherical shell modeled on the Earth s outer core This model performs a magnetohydrodynamics MHD simulation in a rotating spher ical shell modeled on the Earth s outer core see Figure I We consider a spherical shell from the inner core boundary ICB to the core mantle Boundary CMB in a rotating frame which constantly rotates with angular velocity 2 22 The fluid shell is filled with a conductive fluid with constant diffusivities kinematic viscosity v magnetic diffusivity n thermal diffusivity xr and compositional diffusivity xc The inner core 0 lt r lt r is solid and may be considered an electrical insulator or may have the same conductivity as the outer core We assume that the region outside of the core is an electrical insulator The rotating spherical shell is filled with Boussinesq modeled fluid The governing equations of the MHD dynamo problem are the following 1 wxu v P4502 lt x 0 xu p 1 29 2 x u g J x B Po Po 9 pn nVxVxB Vx uxB OT g ET KrV T gr OC ar VIC KOV C 40 V u V B 0 w Vxu and 1 J V xB Ho where u w P B J T C qr and qc are the velocity vorticity pressure magnetic field current density temperature compositional variation heat source and source of light element respectiv
5. 71 i step field ctl ISTEP FIELD Increment of time step to output field data for visualization ISTEP FIELD is defined by integer If ISTEP_ FIELD is set to be 0 no field data are written dt_ctl DELTA TIME Length of time step At is defined by real value time init_ct l INITIAL TIME Initial time to is defined by real value This value is ignored if simulation starts from restart data A 10 restart file ctl Initial field for simulation is defined in this block Back to control MHD rst cti INITIAL_TYPE Type of Initial field is defined by text The following parameters are available for INITIAL TYPE No data No initial data file Small temperature perturbation and seed magnetic field are set as an initial field start fromrst file Initial field is read from spectrum data file File prefix is defined by restart file prefix Dynamo_benchmark_0 Generate initial field for dynamo benchmark case 0 Dynamo benchmark 1 Generate initial field for dynamo benchmark case I Dynamo_benchmark_2 Generate initial field for dynamo benchmark case 2 Pseudo vacuum benchmark Generate initial field for pseudo vacuum dynamo bench mark A 11 time loop ct1 Time evolution scheme is defined in this block Back to control MHD 12 scheme _ctl EVOLUTION SCHEME Time evolution scheme is defined by text Current
6. Direction radial ormeridional issetin Direction and number of subdomains Ndomain are defined in the integer field num domain legendre Direction Ndomain Definition of number of subdomains for Legendre transform between r 0 m and r l m Direction radial or zonal issetin Direction and number of subdomains Ndomain are defined in the integer field num_domain_spectr Direction Ndomain Definition of number of subdomains for spectrum data in r l m Direction modes is set in the Direction field and number of subdomains Ndomain are defined in the integer field A 14 num_grid_sph Spatial resolution of the spherical shell is defined in this block Back to control sph shell 76 truncation_level_ctl Lmax Truncation level L is defined by integer Spherical harmonics is truncated by triangular 0 lt l lt Land0 lt m lt l ngridmeridonal ctl Ntheta Number of grid in the meridional direction Ntheta is defined by integer ngrid_zonal_ctl Nphi Number of grid in the zonal direction Nphi is defined by integer raidal grid typectl explicit Chebyshev or equi_distance Type of the radial grid spacing is defined by text The following types are supported in Calypso explicit Equi distance grid Chebyshev Chebyshev collocation points equi distance Set explicitly by r_layer array num fluid grid ctl Nr shell This option works with radial grid type ctlisexplicit or Che
7. 90 15 16 17 Public License you may choose any version ever published by the Free Software Foundation If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used that proxy s public statement of acceptance of a version permanently authorizes you to choose that version for the Program Later license versions may give you additional or different permissions However no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version Disclaimer of Warranty THERE IS NO WARRANTY FOR THE PROGRAM TO THE EXTENT PER MITTED BY APPLICABLE LAW EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PARTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IM PLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PAR TICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PER FORMANCE OF THE PROGRAM IS WITH YOU SHOULD THE PROGRAM PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SER VICING REPAIR OR CORRECTION Limitation of Liability IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER PARTY WHO MODIFIES AND OR CONVEYS THE PROGRAM AS PERMITTED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPE CIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES
8. If you convey a covered work knowingly relying on a patent license and the Cor responding Source of the work is not available for anyone to copy free of charge and under the terms of this License through a publicly available network server or other readily accessible means then you must either 1 cause the Corresponding Source to be so available or 2 arrange to deprive yourself of the benefit of the patent license for this particular work or 3 arrange in a manner consistent with the requirements of this License to extend the patent license to downstream recipi ents Knowingly relying means you have actual knowledge that but for the patent license your conveying the covered work in a country or your recipient s use of the covered work in a country would infringe one or more identifiable patents in that country that you have reason to believe are valid Tf pursuant to or in connection with a single transaction or arrangement you convey or propagate by procuring conveyance of a covered work and grant a patent license to some of the parties receiving the covered work authorizing them to use propagate modify or convey a specific copy of the covered work then the patent license you grant is automatically extended to all recipients of the covered work and works based on it A patent license is discriminatory if it does not include within the scope of its coverage prohibits the exercise of or is conditioned on the non
9. domain fst Distributed Output 15 1 Format of control file Control file consists the following groups assemble_control e data_files_def Detail num_subdomain_ctl Num PE Detail sph file prefix sph prefix Detail restart file prefix rst prefix Detail e new data files def Detail num new domain ctl new num domain Detail new sph mode prefix new sph prefix Detail new restart prefix new rst prefix Detail delete original data flag YES or NO Detail e control time step ctl Detail i step init ctl integer Detail i step finish ctl integer Detail 57 i step rst ctl integer Detail e newrst magne ctl Detail magnetic field ratio ctl ratio Detail 16 Module dependency program module dependency This program is only used to generate Makefile in work directory Most of case Fortran 90 modules have to compiled prior to be referred by another fortran90 routines This program is generates dependency lists in Makefile To use this program the following limitation is required e One source code has to consist of one module e The module name should be the same as the file name 17 Visualization using field data The field data is written by XDMF or VTK data format using Cartesian coordinate In this section we briefly introduce how to display the radial magnetic field using ParaView as an example After the starting
10. 17 6 4 Doxygen Doxygen http www doxygen org 1is an powerful document generation tool from source files We only save a configuration file in this directory because thousands of html files generated by doxygen The documents for source codes are generated by the follow ing command ed CALYPSO HOME doxygen doxygen Doxyfile CALYPSO 5 5 The html documents can see by opening CALYPSO_HOME doxygen html index html Automatically generated documentation is also available on the CIG website at http www geodynamics org cig software calypso 6 5 Install using configure command 6 5 1 Configuration using configure command Calypso uses the configure script for configuration to install The simplest way to install programs is the following process in the top directory of Calypso Spwd CALYPSO HOME configure o make o make install After the installation object modules can be deleted by the following command make clean configure generates a Makefile in the current directory Available options for configure can be checked using the configure help command The following options are available in the configure command Optional Features disable option checking ignore unrecognized nable with options disable FEATURE do not include FEATURE same as nable FEATURE no enable FEATURE ARG include FEATURE ARG yes enable fftw3 Use fftw3 library 18 Op
11. Detail Layer Radius Detail Layer Boundary_name gen_sph_grid generates indexing table of the spherical transform To perform spheri cal harmonics transform with distributed memory computers data communication table is also included in these files Calypso needs four indexing data for the spherical transform sph_prefix domain rj Indexing table for spectrum data f r 1 m to cal culate linear terms In program spherical harmonics modes l m is indexed by j 1 1 1 m The spectrum data are decomposed by spherical harmonics modes j Data communication table for Legendre transform is included The data also have the radial index of the ICB and CMB sph_prefix domain 11m Indexing table for spectrum data f r l m for Legendre transform The spectrum data are decomposed by radial direction r and spherical harmonics order m Data communication table to caricurate liner terms is included sph prefix domain rtm Indexing table for data f r 0 m for Legendre transform The data are decomposed by radial direction r and spherical harmonics order m Data communication table for backward Fourier transform is included sph prefix domain rtp Indexing table for data f r 0 m for Fourier trans form and field data f r 0 The data are decomposed by radial direction r and meridional direction 0 Data communication table for forward Legendre transform 1s included 9 4 Finite element mesh
12. These boundary conditions are defined by using single external data file See Section 10 3 3 Acknowledgements Calypso was primarily developed by Dr Hiroaki Matsui in collaboration with Prof Bruce Buffett at the University of California Berkeley The following NSF grants supported the development of Calypso e B A Buffett NSF EAR 0509893 Models of sub grid scale turbulence in the Earths core and the geodynamo 2005 2007 e B A Buffett and D Lathrop NSF EAR 0652882 CSEDI Collaborative Research Integrating numerical and experimental geodynamo models 2007 2009 e B A Buffett NSF EAR 1045277 Development and application of turbulence mod els in numerical geodynamo simulations 2010 2012 4 Citation Computational Infrastructure for Geodynamics CIG and the Calypso developers are making the source code to Calypso available to researchers in the hope that it will aid their research and teaching A number of individuals have contributed a significant amount of 7 time and energy into the development of Calypso We request that you cite the appropriate papers and make acknowledgements as necessary The Calypso development team asks that you cite the following papers Matsui H E King and B A Buffett Multi scale convection in a geodynamo simu lation with uniform heat flux along the outer boundary to be submitted to Geochemistry Geophysics Geosystems 5 Model of Simulation 5 1 Governing equations
13. boundary_condition Boundary condition are defined in this block Back to control MHD 63 Table 13 List of field name Name field name Description velocity Velocity u vorticity Vorticity v Vxu pressure Pressure P temperature Temperature T perturbation_temp Perturbation of temperature O T To heat_source Heat source ar composition Composition variation C composition_source Composition source de magnetic_field Magnetic field B current_density Current density J VxB electric field Electric field E 0 J ux B viscous diffusion Viscous diffusion vVxVxu buoyancy Thermal buoyancy arTg composite_buoyancy Compositional buoyancy acCg Lorentz force Lorentz force J x B Coriolis force Coriolis force 202 x u thermal_diffusion Termal diffusion Kp V T grad_temp Temperature gradient VT heat flux Advective heat flux uT composition_diffusion Compositional diffusion KoV2C grad_composition Composition gradient VC composite flux Advective composition flux ul magnetic diffusion Magnetic diffusion nV xVx B poynting flux Poynting flux Ex B rot Lorentz force Curl of Lorentz force V x J x B rot Coriolis force Curl of Coriolis force 20V x 2 x u rot_buoyancy Curl of thermal buoyancy V x arTg rot_composite_buoyancy Curl of compositional buoyancy V x acCg buoyancy_flux Buoyancy flux arTg u Lorentz work Work of Lorentz force u J x B 64 Table 14 Li
14. bug fixes and additional comments for Doxygen are completed The following large bugs are fixed configure command is updated to find appropriate GNU make command see Section Label for radial grid type in the file ctl sph shellraidal grid type ctl is changed to radial_grid_type_ctl If the old name is used in the control file program gen_sph_grid will crash And the following features are implemented New ordering is used for spherical harmonics data to reduce communication time The old version of spectrum indexing data which is generated by gen_sph_grids in Ver 1 0 is also supported in Ver 1 1 e Evaluation of Coriolis term is updated Now Adams Gaunt integrals are evaluated in the initialization process in the simulation program sph_ mhd so the data file for Adams Gaunt integrals which is made by gen_sph_grids is not required e Add a program sph_add_initial_field to modify existed initial field data This program is used to modify or add new fields in spectrum data See Section 13p e Heat and composition source terms are implemented These source terms are fixed with time and defined as spectrum data The source terms are defined by using initial field generation program sph_initial_field or sph add initial field See section and 13p e The boundary conditions for temperature and composition can be defined by using spherical harmonics coefficients i e inhomogeneous boundary conditions can be applied
15. data and order of the field If you change the configuration of data output structure please move the old spectrum monitor file to another directory before starting the programs If a vector field FF is not a solenoidal field F is described by the spherical harmonics coefficients of the poloidal Fg toroidal Fry and potential y components as 10 De l m m m m F r0 GA D V x V x EP Vo ER V OTY l 1 m l In Calypso the following coefficients are written for the non solenoidal vector 48 r Ogi Fo Tan for 170 field name pol Ar 1 Or Spee for 1 0 OF sf m field_name _dpdr r for 170 0 for 1 0 field name tor Eri 49 11 Data transform program sph_snapshot and sph_zm snapshot Input data Program Output data Parallel Spectr index data Spectr data Initial field FEM mesh data Figure 7 Data flow for data transform program Field data VTK or XDMF Simulation program outputs spectrum data as a whole field data This program gen erates field data from spectrum data for visualization This program also can pick Gauss coefficients mean square data over sphere or each surface from spectrum data as the sim ulation program This program requires control file control_snapshot File format of the control file is same as the control field for simulation The same files as the simulation program are read in this program and field data ar
16. directory which is automatically used to complete the compilation The object file and libraries are compiled in the work directory Finally the executive files are assembled in bin directory You should find the following programs in the bin directory gen_sph_grids Preprocessing program for data transfer for spherical transform 19 sph_mhd Simulation program sph_initial_field Example program to generate initial field sph_add_initial_field Example program to add initial field in existing spec tum data sph_snapshot Data transfer from spectrum data to field data sph_dynamobench Data processing for dynamo benchmark test by Christensen ef al 2002 sph_zm_snapshot Generate zonal mean field assemble_sph Data transfer program to change number of subdomains make_f90depends Program to generate dependency of the source code make command uses to generate work Makefile The following library files are also made in work directory libcalypso a Calypso library libfftpack 5d a FFTPACK 5 1 library 6 5 3 Clean The object and fortran module files in work directory is deleted by typing make clean This command deletes files with the extension o mod par diag and 6 5 4 Install The executive files are copied to the install directory INSTDIR bin The install di rectory INSTDIR is defined in Makefile and can also set by prefix option for configure command Alternativel
17. does not have MPI implementation you need to define the definition of MPI libraries MPICHDIR MPICHINCDIR and MPILIBS AR Command name for archive program ex ar to generate libraries If you need some options for archive command options are also included in this valuable RANLIB Command name for ranlib to generate index to the contents of an archive If system does not have ranlib set true in this valuable true command does not do anything for libraries F900OPTFLAGS Optimization flags for Fortran90 compiler including OpenMP flags 21 FFTW3_CFLAGS Option flags for FFTW3 ex 1 usr local include FFTW3_LIBS Library lists for FFTW3 ex L usr local 1 hfd5 command h5pf h5pfe show Ju b 1fftw3 1m HDF5 FFLAGS Option flags to compile with HDF5 This setting can be found by using c show HDF5 LDFLAGS Option flags to link with HDF5 This setting can be found by using hfd5 command h5pfe show HDF5 FLIBS Library lists for HDFS This setting can be found by using hfd5 command 6 7 Install using cmake CMake is a cross platform open source build system CMake can be downloaded from http www cmake org The following procedure is required to install 1 Create working directory you can also use CALYPSO_HOME work 2 Generate Makefile and working directories by cmake command 3 Compile programs by In this section CALY
18. exercise of one or more of the rights that are specifically granted under this License You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software under which you make payment to the third party based on the extent of your activity of conveying the work and under which the third party grants to any of the parties who would receive the covered 89 12 13 14 work from you a discriminatory patent license a in connection with copies of the covered work conveyed by you or copies made from those copies or b primarily for and in connection with specific products or compilations that contain the covered work unless you entered into that arrangement or that patent license was granted prior to 28 March 2007 Nothing in this License shall be construed as excluding or limiting any implied li cense or other defenses to infringement that may otherwise be available to you under applicable patent law No Surrender of Others Freedom If conditions are imposed on you whether by court order agreement or otherwise that contradict the conditions of this License they do not excuse you from the con ditions of this License If you cannot convey a covered work so as to satisfy simul taneously your obligations under this License and any other pertinent obligations then as a consequence you may not convey it at all For example if you agree to terms that ob
19. field data for visualize snapshots fld prefix is defined by text Step number and file extension are added after this file prefix field file fmt ctl fld_ format Field data field format for visualize snapshots fld format is defined by text The following formats are currently supported 62 single HDF5 Merged HDFS file Available if HDF5 library is linked single VTK Merged VTK file Default VTK Distributed VTK file A2 phys values ctl Fields for the simulation are defined in this block Back to control MHD array nod value ctl Field Viz flag Monitor flag Fields name Field for the simulation are listed in this array If required fields for simulation are not in the list simulation program adds required field in the list but does not output any field data and monitoring data Viz flag is set to output of the field data for visualization by VIz On Write field data to VTK file VIz Off Do not write field data to VTK file In the Monitor flag output in the monitoring data is defined by Monitor On Write spectrum into monitoring data Monitor Off Do not write spectrum into monitoring data Supported field in the present version is listed in Table 13 A 3 timeevolutionctl Fields for time evolution are defined in this block Back to control MHD array time_evo_ctl Field Fields name for time evolution are listed in this array in Field by text Available fields are listed in Table 14 A4
20. initial fields for dynamo benchmark can set in the simulation program by setting INITIAL TYPE flag This program is used to generate initial field by user The heat source qr and light element source qc are also defined by this program because qr and qc are defined as scalar fields The Fortran source file to define initial field const_sph_initial_spectr f90issavedinsrc programs data_utilities INITIAL_FIELD directory and please compile again after modifying this module This program also needs the files listed in Table 9 This program generates the spectrum Table 9 List of files for simulation sph initial field name Parallelization I O control MHD Serial Input sph_prefix domain rj Distributed Input sph prefix domainf rim Distributed Input sph prefix domainf rtm Distributed Input sph_prefix domain rtp Distributed Input rst_prefix 0 domain fst Distributed Input Output data files rst_prefix 0 domain fst To use generated initial data file 52 please set ISTEP_START to be 0and INITIAL TYPE to be start from rst file 13 Initial field modification program sphadd initial field Input data Program Output data Parallel Spectr index data Spectr data Snapshots data Figure 9 Data flow for initial field modification program Caution This program overwrites existing initial field da
21. prefix field fil e prefix field fil e fmt ctl e model phys values ct1l Detail x array nod value ctl Detail time _evolution_ctl Detail array time evo ctl boundary condition l Detail array bc temperature ANI w AN w AN w Detail rray bc_velocity Detail rray bc_composition Detail rray bc_magnetic_field Detail forces_define Detail 36 Num PE Detail Num Threads Detail sph prefix Detail D is described below The detail of each block boundary data name rst prefix Detail f f Field ld prefix Detail 1d format Detail Viz flag Field Detail Gro Gro Gro Gro Type Type Type Type Monitor flag array force ctl Force Detail dimensionless_ct1 Detail array dimless_ctl Name Value Detail coefficients_ct1 Detail x thermal Detail array coef 4 termal ctl Name Power Detail Detai 1 D IAN array coef 4 t diffuse ctl Name Power array coef 4 heat source ctl Name Pow tail x moment um Detail array coef 4 velocity_ctl Name Power Detail 0 K O I array coef 4 press_ctl Name Power Detail array coef 4 v diffuse ctl Name Power Detail array coef 4 buoyancy ctl Name Power Detail vu vi Nr array
22. program An example for spectrum data assembling program is provided in assemble_sph di rectory 8 4 Example of heat and compositional source An example to perform a simulation with heat and compositional sources is given in heat composition source directory To simplify the problem only the thermal and compositional fields are evolved with no velocity i e pure diffusion problem A module to generate initial field data const sph initial spectriscopiedtosrc programs data utilities NITIAL FIELD directory The code must be recompiled after modifying this mod ule Initial field is generated by the program sph initial field after generating spherical harmonics information by gen sph grid Aftrer the simulation Y com ponent of temperature and composition as a function of radius and time is written in picked mode dat 8 5 Example of thermal and compositional boundary conditions by external file Heterogeneous boundary are input using an external file An example to set thermal and compositional boundary conditions is given in heterogineous temp directory As in the heat source example only the diffusion problem is solved in this example In file bc spectr btx temperature boundary conditions are defined for Y YS Y and Y component and compositional boundary is defined for Y Y S and Y components The radial profile of these spherical harmonics coefficients are written in picked_mode dat 29 9 Prep
23. program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this program If not see lt http www gnu org licenses gt Also add information on how to contact you by electronic and paper mail If the program does terminal interaction make it output a short notice like this when 1t starts in an interactive mode lt program gt Copyright C lt year gt lt name of author gt This program comes with ABSOLUTELY NO WARRANTY for details type show w This is free software and you are welcome to redistribute it under certain conditions type show c for details 92 The hypothetical commands show w and show c should show the appropriate parts of the General Public License Of course your program s commands might be different for a GUI interface you would use an about box You should also get your employer if you work as a programmer or school if any to sign a copyright disclaimer for the program if nece
24. sph add initial field 53 14 Check program for dynamo benchmark 54 EET 54 15 Data assemble program assemble sph 56 15 1 Format of control filel a aoa a 57 58 58 62 62 DEN eenen NE 62 me SOE e oe a e ee 63 SA O 63 ee eto ae eee bees 63 FE PT er Pe re a re EN 67 bce sich ah ae bee SAT Gace ae ee a ei 67 pce dae eee ae an Sa a eae Ae 68 AL thermal 6 25 a oe Ste baw as hee Rake Ye eke 68 EE eee 68 sre Bs es hs ee en ee de en do We Bd 69 EE Gude act de Ennn aia 70 A eee a es e EA 70 A 9 time step CCl sep aen ete ls Boke ta de ke Bk Ga Eede a 71 RE Rn B Me ee 72 AT time LOOSE ll zes an rn rr ra he hoch B 72 ARE ETEN ES ES ENEN EN 74 A 13 num domain Ct 76 NEN 76 ARA 78 gk pub A mee ee eee S 79 79 1 Introduction Calypso is a program package for magnetohydrodynamies MHD simulations in a ro tating spherical shell for geodynamo problems This package consists of the simulation program preprocessing program post processing program to generate field data for visu alization programs and several small utilities The simulation program runs on parallel computing systems using MPI and OpenMP parallelization Calypso solves the equations that govern convection and magnetic field generation in a rotating spherical shell Flow is driven by thermal or compositional buoyancy in a Boussi nesq fluid Calypso also support various boundary conditions e g fixed temperature heat flux compo
25. to output spectrum data are listed in Degree by integer All spectrum data with listed degree I is output in file array pick_sph_order_ctl Order Order m to output spectrum data are listed in Order by integer All spectrum data with listed order m is output in file array pick_gauss_coefs_ctl Degree Order List of spherical harmonics mode I and m of Gauss coefficients to output Degree and Order are defined by integer array pick gauss coef degree ctl Degree Degrees to output Gauss coefficients are listed in Degree by integer All Gauss coefficients with listed is output in file 75 array pick gauss coef order ctl Order Orders m to output Gauss coefficients are listed in Order by integer All Gauss coef ficients with listed order m is output in file nphimidegctl Nphi mid equator Number of grid points Nohi mid equator in longitudinal direction to evaluate mid depth of the shell in the equatorial plane for dynamo benchmark is defined as integer If Nphi mid equator is not defined or less than zero Nohi mid equator is set set number grid as the input spherical transform data A13 num domain ctl1l Parallelization is defined in this block Domain decomposition is defined for spectrum data field data and Legendre transform Back to control sph shell num_domain_sph grid Direction Ndomain Definition of number of subdomains for physical data in spherical coordinate r 0
26. you this License giving you legal permission to copy distribute and or modify it For the developers and authors protection the GPL clearly explains that there is no warranty for this free software For both users and authors sake the GPL requires that modified versions be marked as changed so that their problems will not be attributed erroneously to authors of previous versions Some devices are designed to deny users access to install or run modified versions of the software inside them although the manufacturer can do so This is fundamen tally incompatible with the aim of protecting users freedom to change the software The systematic pattern of such abuse occurs in the area of products for individuals to use which is precisely where it is most unacceptable Therefore we have designed this version of the GPL to prohibit the practice for those products If such problems arise substantially in other domains we stand ready to extend this provision to those domains in future versions of the GPL as needed to protect the freedom of users Finally every program is threatened constantly by software patents States should not allow patents to restrict development and use of software on general purpose com puters but in those that do we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary To prevent this the GPL assures that patents cannot be used to render the program non
27. 8E 001 1 930213889461227E 000 3 501010216256124E 00 0 5 071806543051021E 000 7 808553595635292E 001 1 64958344 1437563E 001 5 136522824340612E 000 8 047915942925034E 000 3 752181234262930E 001 15 Data assemble program assemble sph Input data Program Output data Serial Spectr index data Spectr data Initial field New spectr index data Spectr data Snapshots data Figure 10 Data flow for spectrum data assemble program Calypso uses distributed data files for simulations This program is to generate new spectrum data for restarting with different spatial resolution or parallel configuration This program organizes new spectral data by using specter indexing data using different domain decomposition The following files used for data IO If radial resolution is changed from the original data the program makes new spectrum data by linear interpolation If new 56 data have smaller or larger truncation degree the program fills zero to the new spectrum data or truncates the data to fit the new spatial resolution respectively Data files for the program are shown In Table 12 and definition of control assemble sphis Table 12 List of files for assemble_sph extension Distributed I O control_sph_assemble Serial Input sph_prefix domain rj Distributed Input new sph prefix domainf rj Distributed Input rst_prefix step domain fst Distributed Input new_rst_prefix step
28. A Takahashi F Tilgner A Wicht J and Zhang K A numerical dynamo benchmark Physics of the Earth and Planetary Interiors 128 25 34 2001 61 Appendix A Definition of parameters for control files A l data files def File names and number of processes and threads are defined in this block Back to control MHD Back to control sph shell Back to control assemble sph num_subdomain_ctl Num PE Number of subdomain for the MPI program Num PE is defined by integer If number of processes in mpirun np is different from number of subdomains program will be stopped with message num_smp_ctl Num Threads Number of SMP threads for OpenMP Num Threads is defined by integer You can set larger number than the actual umber of thread to be used If actual number of thread is less than this number number of threads is set to the number which is defined in this field sph file prefix sph prefix File prefix of spherical harmonics indexing and FEM mesh file sph prefix is de fined by text Process ID and extension are added after this file prefix boundary data file name boundary data name File name of boundary condition data file boundary data name is defined by text restart file prefix rst prefix File prefix of spectrum data for restarting and snapshots rst prefix is defined by text Step number process ID and extension are added after this file prefix field file prefix fld prefix File prefix of
29. ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSI BILITY OF SUCH DAMAGES Interpretation of Sections 15 and 16 If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms reviewing courts shall apply local 91 law that most closely approximates an absolute waiver of all civil liability in con nection with the Program unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program and you want it to be of the greatest possible use to the public the best way to achieve this is to make it free software which everyone can redistribute and change under these terms To do so attach the following notices to the program It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty and each file should have at least the copyright line and a pointer to where the full notice is found lt one line to give the program s name and a brief idea of what it does gt Copyright C lt textyear gt lt name of author gt This
30. COMPUTATIONAL INFRASTRUCTURE FOR GEODYNAMIGS GIG User Manual Version 1 1 Hiroaki Matsui www geodynamics org Preface Calypso is a program package of magnetohydrodynamics MHD simulations in a rotating spherical shell for geodynamo problems This package consists of the simulation program preprocessing program post processing program to generate field data for visualization programs and several small utilities The simulation program runs on parallel computing systems using MPI and OpenMP parallelization Contents 1 Introduction N 2 1 History Updates for Ver LN oo ar AA a 3 Acknowledgements Citation 5 Model of Simulation 5 1 Governing equations e e ee 5 2 Spherical harmonics expansion 22 ark vr kr e 5 3 Evaluation of Coriolis terMdl 5 4 Boundary conditions rv kr kran 5 4 1 Non slip boundary o rn rn av 5 4 2 Free slip boundary 54 3 Fixedrotationrate ee ee A A A A ie a A NE ep vet ak ce ae alae whee ae le 5 4 8 Connection to the magnetic potential field ee Be Gas sno dn 6 Installation 6 1 Library Requirements sert er RR RR AR 6 2 Known problems 625625 eee ee ee ee lt lt 6 3 Dreta OE ORV Ge Ole ae dra a A ne ot B ante 6 5 Install using configure command 6 5 1 Configuration using configure command
31. MHD coef 4 velocityctl ae ae ee i u w ia i Coefficient for evolution of velocity DE or DE for the vorticity equation and advection w x u or V x w x u for the vorticity equation is defined by this array 68 coef 4 press ctl Name Power Coefficient for pressure gradient VP is defined by this array Pressure does not appear the vorticity equation which is used for the time integration But this coefficient is used to evaluate pressure field coef 4 v diffuse ctl Name Power Coefficient for viscous diffusion vV x V x u is defined by this array coef 4 buoyancy ctl Name Power Coefficient for buoyancy arT g is defined by this array coef 4 Coriolis ctl Name Power Coefficient for Coriolis force 202 x u is defined by this array coef_4_Lorentz_ctl Name Power Coefficient for Lorentz force py J x B is defined by this array coef 4 composit buoyancy ctl Name Power Coefficient for compositional buoyancy acCg is defined by this array A 7 3 induction Coefficients of each term in magnetic induction equation are defined in this block Back to control MHD coef_4 magnetic ctl Name Power B Coefficient for evolution of temperature is defined by this array Ot coef_4_m_diffuse_ctl Name Power Coefficient for magnetic diffusion 7V x V x B is defined by this array coef 4 inductionctl Name Power Coefficient for magnetic induction V x u x B is define
32. PSO make command HOME work is used as the working directory Options for CMake can be checked by cmake i CALYPSO HOME command at CALYPSO HOME work There are a number of options can be found but the following valuables are 1m portant settings for installation CMAKE_ INSTALL PREF X Install directory CMAKE_Fortran_COMP ILER Fortran90 compiler is set in this valuable CMAKE DISABLE FIND PACKAGE OpenMP Fortran OpenMP is not used if yes set in this valuable CMAKE_LIBRARY_PATH FFTW3 library CMAKE_DISABLE_FIND_PACKAGE_FFTW FFTW3 library does not linked if yes is CMake library search paths This directory is used to search 22 CMAKE INCLUDE PATH CMake include search paths This directory is used to search include file for FFTW3 CMAKE DISABLE FIND PACKAGE FFTW FFTW3 library does not linked if yes is set in this valuable HDF5 INCLUDE DIRS Include file directories to compile with HDF5 This setting can be found by using hfd5 command h5pfe show HDF5 LIBRARY DIRS Location of HDFS library This setting can be found by using hfd5 command h5pfc show HDF5 LIBRARIES Library lists for HDF5 This setting can be found by using hfd5 command h5pfc show CMAKE DISABLE FIND PACKAGE HDF5 HDES library does not linked if yes is set in this valuable An example of usin
33. Paraview the file to be read is chosen in the file menu and press apply button Then Paraview load the data from files see Figure 11 Because the magnetic field is saved by the Cartesian coordinate the radial magnetic field is obtained by the calculator tool The procedure is as following see Figure I2 1 Push calculator button 2 Choose Point Data in Attribute menu 3 Input data name for radial magnetic field B_r in Figure 12 4 Enter the equation to evaluate radial mantic field B B r r Nn Finally push Apply button After obtaining the radial mantric field the image in figure I3 is obtained by using slice and Contour tools with appropriate color mapping 58 Hil ParaView 3 98 0 64 bit ae Se oo e ml GE amp KA DP D Pi FH Time E e ER Representation p ig gt de de at zt de KAK S9GVsSEOELASDBS mm Properties Information Pipeline Browser ETTER ____ oo Properties AO Eo 18 D Reset 3 Delete Search 25 Open File open multiple files with lt ctrl gt key 3 Load selected file Look in Kemo_MB_Retina Filename 9 home gt 5 out xdmf Gi net out solution xdmf 9 MobileBackups E pub_e 2 Select file to input UN Time Machine K vtk or xdmf format 3 sph_case1_25 Gi field 4 Gi field Bi field OG psf 2m rot
34. _name to Center Inner boundary of the domain to fill the center ICB ICB CMB CMB A 15 new data files def File names and number of processes for new domain decomposed data are defined in this block Back to control_assemble_sph num_new_domain_ctl new num domain Number of subdomain for new new decomposed data new num domain is defined by integer new_sph mode prefix new sph prefix File prefix of new spherical harmonics indexing new sph prefix is defined by text new restart prefix new rst prefix File prefix of new spectrum data new rst prefix is defined by text 78 delete original data flag delete original data flag If this flag set to YES original specter data is deleted at the end of program A 16 newrst magne ctl Parameters to modify magnetic field are defined in this block Back to control assemble sph magnetic field ratio ctl ratio Ratio of new magnetic field data to original magnetic field ratio is defined by real Appendix B GNU GENERAL PUBLIC LICENSE Copyright 2007 Free Software Foundation Inc http fsf org Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed Preamble The GNU General Public License is a free copyleft license for software and other kinds of works The licenses for most software and other practical works are designed to take away your freedom to share and change the works By contras
35. a covered work you waive any legal power to forbid circumven tion of technological measures to the extent such circumvention is effected by exer cising rights under this License with respect to the covered work and you disclaim any intention to limit operation or modification of the work as a means of enforcing against the work s users your or third parties legal rights to forbid circumvention of technological measures Conveying Verbatim Copies You may convey verbatim copies of the Program s source code as you receive it in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice keep intact all notices stating that this License and any non permissive terms added in accord with section 7 apply to the code keep intact all notices of the absence of any warranty and give all recipients a copy of this License along with the Program You may charge any price or no price for each copy that you convey and you may offer support or warranty protection for a fee Conveying Modified Source Versions You may convey a work based on the Program or the modifications to produce it from the Program in the form of source code under the terms of section 4 provided that you also meet all of these conditions a The work must carry prominent notices stating that you modified it and giving a relevant date b The work must carry prominent notices stating that it is released un
36. ajor essential component kernel window system and so on of the specific operating system if any on which the executable work runs or a compiler used to produce the work or an object code interpreter used to run it The Corresponding Source for a work in object code form means all the source code needed to generate install and for an executable work run the object code and 81 to modify the work including scripts to control those activities However it does not include the work s System Libraries or general purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work For example Corresponding Source includes interface definition files associated with source files for the work and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require such as by intimate data communication or control flow between those subprograms and other parts of the work The Corresponding Source need not include anything that users can regenerate au tomatically from other parts of the Corresponding Source The Corresponding Source for a work in source code form is that same work Basic Permissions All rights granted under this License are granted for the term of copyright on the Program and are irrevocable provided the stated conditions are met This License explicitly affirms your unlimited per
37. al grids is set as the outermost loop Long_loop Long one dimentional loop is used A12 sphmonitor ctl Monitoring data is defined in this block Monitoring data output root mean square av erage Gauss coefficients or specific components of spectrum data which are flagged by Monitor On in nod value ct1l array Back to control MHD volume average prefix vol ave prefix File prefix for volume average data vol ave prefix is defined by Text Program add dat extension after this file prefix If this file prefix is not defined volume average data are not generated volume pwr_spectr prefix vol pwr prefix File prefix for mean square spectrum data averaged over the fluid shell vol pwr prefix is defined by Text Spectrum as a function of degree I is written in vol pwr prefix 1 dat spectrum as a function of order m is written in vol pwr prefix m dat and spec trum as a function of l m is written in vol pwr prefix 1lm dat This prefix is also used for the file name of the volume mean square data as vol pwr prefix dat If this file prefix is not defined volume spectrum data are not generated and volume mean square data is written as sph pwr volume dat layered pwr_spectr prefix layer pwr prefix File prefix for mean square spectrum data averaged over each sphere surface layer pwr prefix is defined by Text Spectrum as a function of degree I is written in layer pwr prefix 1 dat spectrum as a fu
38. am or any portion of it Patents A contributor is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based The work thus licensed is called JG the contributor s contributor version A contributor s essential patent claims are all patent claims owned or controlled by the contributor whether already acquired or hereafter acquired that would be 88 infringed by some manner permitted by this License of making using or selling its contributor version but do not include claims that would be infringed only as a consequence of further modification of the contributor version For purposes of this definition control includes the right to grant patent sublicenses in a manner consistent with the requirements of this License Each contributor grants you a non exclusive worldwide royalty free patent license under the contributor s essential patent claims to make use sell offer for sale im port and otherwise run modify and propagate the contents of its contributor version In the following three paragraphs a patent license is any express agreement or commitment however denominated not to enforce a patent such as an express per mission to practice a patent or covenant not to sue for patent infringement To grant such a patent license to a party means to make such an agreement or com mitment not to enforce a patent against the party
39. ansfer of a copy is not conveying An interactive user interface displays Appropriate Legal Notices to the extent that it includes a convenient and prominently visible feature that 1 displays an appro priate copyright notice and 2 tells the user that there is no warranty for the work except to the extent that warranties are provided that licensees may convey the work under this License and how to view a copy of this License If the interface presents a list of user commands or options such as a menu a prominent item in the list meets this criterion Source Code The source code for a work means the preferred form of the work for making modifications to it Object code means any non source form of a work A Standard Interface means an interface that either is an official standard defined by a recognized standards body or in the case of interfaces specified for a particular programming language one that is widely used among developers working in that language The System Libraries of an executable work include anything other than the work as a whole that a is included in the normal form of packaging a Major Component but which is not part of that Major Component and b serves only to enable use of the work with that Major Component or to implement a Standard Interface for which an implementation is available to the public in source code form A Major Component in this context means a m
40. byshev Number of layer in the fluid shell Nr shell is defined by integer Number of grids including CMB and ICB will be INr shell 1 fluid core size ctl Length This option works with radial grid type ctlisexplicit or Chebyshev Size of the outer core Length ro r is defined by real ICB to CMB ratio ctl R ratio This option works with radial grid type ctlisexplicit or Chebyshev Ratio of the inner core radius to outer core R_ratio r r is defined by real Min_radius_ctl Rmin This option works with radial grid type ctlisexplicit or Chebyshev Minimum radius of the domains Rmin is defined by real If this value is not defined ICB becomes inner boundary of the domain TT Max_radius_ctl Rmax This option works with radial grid type ctlisexplicit or Chebyshev Maximum radius of the domains Rmax is defined by real If this value is not defined CMB becomes outer boundary of the domain r layer Layer Radius This option works with radial_grid_type_ct1 isexplicit List of the ra dial grid points in the simulation domain Index of the radial point Layer is defined by integer and radius Radius is defined by real array boundaries ctl Boundary name Layer This option works with radial grid type ctl is explicit Boundaries of the simulation domain is defined by Layer in r layer array The following boundary name can be defined for Boundary
41. cal shell boundaries Consequently radial current density J vanishes at the boundary as J f Sater r fro In an electrical insulator the magnetic field can be described as a potential field Bext V West where Wet is the magnetic potential The boundary conditions can be satisfied by con necting the magnetic field in the fluid shell at boundaries to the potential fields The mag netic field is connected to the potential field in an electrical insulator At CMB r ro the boundary condition can be described by the poloidal and toroidal coefficients of the magnetic field as l OBS Bm Ef el me r Ape and If the inner core is also assumed to be an insulator the magnetic boundary conditions for ICB r r can be described as ee pel baer A OB gr N r Des and 14 5 4 9 Magnetic boundary condition for center If the inner core has the same conductivity as the outer core we solve the induction equa tion for the inner core as for the outer core with the boundary conditions for the center The poloidal and toroidal coefficients at center are set to By 0 Br 0 0 5 4 10 Pseudo vacuum magnetic boundary condition Under the pseudo vacuum boundary condition the magnetic field has only a radial com ponent at the boundaries Considering the conservation of the magnetic field the magnetic boundary condition will be gt Dr r Be Be B Q atr ri To The present boundary condition is als
42. cense from a partic ular copyright holder is reinstated a provisionally unless and until the copyright holder explicitly and finally terminates your license and b permanently if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation Moreover your license from a particular copyright holder is reinstated permanently 1f the copyright holder notifies you of the violation by some reasonable means this 1s the first time you have received notice of violation of this License for any work from that copyright holder and you cure the violation prior to 30 days after your receipt of the notice Termination of your rights under this section does not terminate the licenses of par ties who have received copies or rights from you under this License If your rights 87 10 11 have been terminated and not permanently reinstated you do not qualify to receive new licenses for the same material under section 10 Acceptance Not Required for Having Copies You are not required to accept this License in order to receive or run a copy of the Program Ancillary propagation of a covered work occurring solely as a con sequence of using peer to peer transmission to receive a copy likewise does not require acceptance However nothing other than this License grants you permission to propagate or modify any covered work These actions infringe copyright if you do not accept this Licens
43. coef 4 Coriolis ctl Name Power Detail array coef 4 Lorentz ctl Name Power J O feb array coef 4 composit buoyancy ctl Name Power Detail x induction Detail array coef 4 magnetic ctl Name Power Detail array coef 4 m diffuse ctl Name Power Detail array coef 4 induction ctl Name Power Detail composition Detail array coef 4 composition ctl Name Power De tail array coef 4 c diffuse ctl Name Power Detail array coef 4 composition source ctl Name Power Detail temperature define Detail ref temp ctl REFERENCE TEMP Detail x low temp ctl Detail depth RADIUS Detail temperature TEMPERATURE Detail 37 x high_temp_ctl Detail depth RADIUS Detail temperature TEMPERATURE Detail O e control time_step_ct1 Detail elapsed_time_ctl ELAPSED TIME x i step init ctl ISTEP START Detail x Step finish etl ISTEP FINISH Detail i step check ctl ISTEP MONITOR i step rst ctl ISTEP RESTART Detail i step field ctl ISTEP FIELD Detail dt ctl DELTA TIME Detail time init ct INITIAL TIME Detail restart file ctli Detail rst ctl INITIAL TYPE Detail time loop ctl Detail scheme ctl EVOLUTION SCHEME Deta
44. d by this array 69 A 7 4 composition Coefficients of each term in composition equation are defined in this block Back to control MHD coef_4_composition_ctl Name Power OC Coefficient for evolution of composition variation DE and advection of heat u V C is defined by this array coef 4 c diffusectl Name Power Coefficient for compositional diffusion k V C is defined by this array coef_4_composition_source_ctll Name Power Coefficient for composition source qc is defined by this array A8 temperature define Reference of temperature To is defined in this block If reference of temperature is defined perturbation of temperature O T To is used for time evolution and buoyancy Back to control MHD ref_temp_ct REFERENCE TEMP Type of reference temperature is defined by text The following options are available for REFERENCE TEMP none Reference of temperature is not defined Temperature 7 is used to time evolution and thermal buoyancy spherical_shell Reference of temperature is set by 1 r r To _ rin raTa EET rn ri r low temp ctl Amplitude of low reference temperature 7 and its radius r Generally r ro are defined in this block high temp ctl Amplitude of high reference temperature 7 and its radius r Gener ally ra r are defined in this block 70 depth RADIUS Radius for reference temperature is defined by real
45. data Calypso generates field data for visualization with XDMF or VTK format To generate field data file the preprocessing program generates FEM mesh data for each subdomain of spherical grid r 0 4 under the Cartesian coordinate x y 2 The mesh data file is writ ten as GeoFEM http geofem tokyo rist or jp mesh data format which consists of each subdomain mesh and communication table among overlapped nodes 9 5 Radial grid data The preprocessing program generates radius of each layer in radial_info dat if radial_grid_type_ctl is set to Chebyshev or equi_distance This file con sists of blocks array r_layerand array boundaries_ctl for control file This data may be useful if you want to modify radial grid spacing by yourself 33 10 Simulation program sph mhd The name of the simulation program is sph mhd This program requires cont rol MHD as a Control file This program performs with the indexing file for spherical harmonics and Coriolis term integration file generated by the preprocessing program gen_sph_grid Data files for this program are listed in Table 3 Indexing data for spherical harmonics Input data Program Output data Spectr data Snapshots data Parallel Spectr index data Spectr data Initial field Field data VTK or XDMF Figure 5 Data flow for the simulation program which starting with sph prefix are obtained by the preprocessing program gen sph grid The bounda
46. der this License and any conditions added under section 7 This requirement modifies the requirement in section 4 to keep intact all notices c You must license the entire work as a whole under this License to anyone who comes into possession of a copy This License will therefore apply along with any applicable section 7 additional terms to the whole of the work and all its parts regardless of how they are packaged This License gives no permission to license the work in any other way but it does not invalidate such permission if you have separately received it d If the work has interactive user interfaces each must display Appropriate Legal Notices however if the Program has interactive interfaces that do not display Appropriate Legal Notices your work need not make them do so 83 A compilation of a covered work with other separate and independent works which are not by their nature extensions of the covered work and which are not combined with it such as to form a larger program in or on a volume of a storage or distribution medium is called an aggregate 1f the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation s users beyond what the individual works permit Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate Conveying Non Source Forms You may convey a covered work in object code fo
47. e Therefore by modifying or propagating a covered work you indicate your acceptance of this License to do so Automatic Licensing of Downstream Recipients Each time you convey a covered work the recipient automatically receives a license from the original licensors to run modify and propagate that work subject to this License You are not responsible for enforcing compliance by third parties with this License An entity transaction is a transaction transferring control of an organization or substantially all assets of one or subdividing an organization or merging organiza tions If propagation of a covered work results from an entity transaction each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party s predecessor in interest had or could give under the previous paragraph plus a right to possession of the Corresponding Source of the work from the predecessor in interest if the predecessor has it or can get it with reasonable efforts You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License For example you may not impose a license fee royalty or other charge for exercise of rights granted under this License and you may not initiate litigation including a cross claim or counterclaim in a lawsuit alleging that any patent claim is infringed by making using selling offering for sale or importing the Progr
48. e generated from the snapshots of spectrum data The monitoring data for snapshots can also be generated step is added in the file name and the step is calculated by time step ISTEP_ FIELD 50 Table 8 List of files for simulation sph_snap and sph_zm_snap name Parallelization I O control snapshot Serial Input sph prefix domainf rj Distributed Input sph prefix domainf rim Distributed Input sph prefix domainf rtm Distributed Input sph prefix domainf rtp Distributed Input sph prefix domain gfm Distributed Input boundary data name Single Input rst_prefix step domain fst Distributed Input vol_pwr_prefix dat Single Output vol_pwr_prefix _l dat Single Output vol pwr prefix m dai Single Output vol pwr prefix lm dat Single Output vol ave prefix dat Single Output ct ct layer pwr prefix 1 dat Single Output layer pwr prefix m dat Single Output layer pwr prefix lm dat Single Output cr GA gauss_coef_prefix dat Single Output picked_sph_prefix dat Single Output CT CT fld_prefix step domain extension Output 51 12 Initial field generation program sph initial field Input data Program Output data Parallel Spectr index data Spectr data Snapshots data Figure 8 Data flow for initial field generation program The
49. e 7 Number of components for each field Labels for data indicates as t_step Time setp number time Time K_ene pol Amplitude of poloidal kinetic energy K_ene_tor Amplitude of toroidal kinetic energy K_ene Amplitude of total kinetic energy M ene pol Amplitude of poloidal magnetic energy M_ene_tor Amplitude of toroidal magnetic energy M_ene Amplitude of total magnetic energy Field pol Mean square amplitude of poloidal component of Field Field tor Mean square amplitude of toroidal component of Field Field Mean square amplitude of Field 44 10 5 1 Volume average data Volume average data are written by defining volume average prefix in control file Volume average data are written in vol ave prefix dat with same format as RMS amplitude data If you need the sphere average data for specific radial point you can use picked spectrum data for I m 0 at specific radius 10 5 2 Volume spectrum data Volume spectrum data are written by defining volume pwr spectr prefix in con trol file By defining volume pwr spectr prefix following spectrum data averaged over the fluid shell is written Data format is the same as the volume mean square data but degree l order m or meridional wave number I m is added in the list of data vol pwr prefix 1 dat Volume average of mean square amplitude of the fields as a function of spherical harmonic degree For scalar field the spectrum is fall 7 X farra m l F
50. ed to use Merged XDMF data generate files listed in Table 7 For ParaView all subdomain data is read by choosing fld prefix solution xdmf in file menu Table 7 List of written files for XDMF format name fld prefix mesh h5 HDES file for geometry data fld prefix step h5 HDES file for field data fld_prefix solution xdmf HDFS file lists to be read 43 10 5 Mean square amplitude data This program output mean square amplitude of the fields which is marked as Monitor ON over the fluid shell at every increment monitor steps For vector fields For the velocity u and magnetic field B the kinetic energy 1 2u and magnetic energy 1 2B are calculated instead of mean square amplitude Labels on the first lines indicate following data The data file have the following headers in the first 7 lines and headers of the data and data are stored in the following lines The header in the first 7 lines is the following If these mean square amplitude data files exist before starting the simulation programs append results at the end of files without checking constancy of the number of data and order of the field If you change the configuration of data output structure please move the existed data files to another directory before starting the programs line 2 Number of radial grid and truncation level line 4 radial layer ID for ICB and CMB line 6 Number of field of data total number of components lin
51. ely Coefficients in the governing equations are the kinetic viscosity v thermal diffusivity kr compositional diffusivity ko and magnetic diffusivity 7 The density p is written as a function of T C average density po thermal expansion ar and density ratio of light element to main composition ac p po 1 ar T To ac C Co In Calypso the vorticity equation and divergence of the momentum equation are used for solving u w and P as OP EV x w xu pVx V xw 2QV x 2 x u p 1 V x g V x J x B Po Po and V wxu V P 51 20V 2x u LV 29 V J x B Po Po 10 5 2 Spherical harmonics expansion In Calypso fields are expanded into spherical harmonics A scalar field for example temperature T r 0 is expanded as T r 0 9 Y Tr 0 0 l 0 m l where Y are the spherical harmonics Solenoidal fields e g velocity u vorticity w magnetic field B and current density J are decomposed into poloidal and toroidal com ponents For example the magnetic field is described as l B r 0 0 Y X Bs Br l 1 m l where Ba r 0 0 VxVx Bg r Y 0 r Brij r 0 Vx Byr r Y 0 p i The spherical harmonics are defined as real functions P cos mg is assigned for positive m Pf sin m is assigned for negative m where P are Legendre polynomi als Because Schmidt quasi normalization is used for the Legendre polynomials Py the
52. fined in Group Real value is required in Value but they value is not used in the program rot inner core If this condition is set inner core r lt r rotation is solved by using viscous torque and Lorentz torque This boundary condition can be used for ICB 65 and grid is filled to center Real value is required in Value but they value is not used in the program rot _x Set constant rotation around z axis in Value by real Rotation vector can be defined with rot_y and rotz rot y Set constant rotation around y axis in Value by real Rotation vector can be defined with rot_z and rot_x rot_z Set constant rotation around z axis in Value by real Rotation vector can be defined with rot x and rot y array be magnetic field Group Type Value Boundary conditions for magnetic field are defined by this array Position of boundary is defined in Group by to Center ICB or CMB The following boundary conditions are available for magnetic field in Type column insulator Magnetic field is connected to potential field at boundary defined in Group real value is required at Value but they value is not used in the program sph_to_center If this condition is set magnetic field in conductive inner core r lt rj 1s solved This boundary condition can be used for 1CB and grid is filled to center The value at Value does not used array bc composition Group Type Value Boundary condi
53. force Users matsui Desktop sph casel 26 test field zl 9 Bw File name out solution xdmf m Files of type Supported Files cml Flash flash bounda Cancel Figure 11 File open window for ParaView 39 MI ParaView 4 0 1 64 bit p Ea GF amp Ka b WD bl B Time 250003 o O B da eer Surface 3 Ds GEM U a S B 5 RRP MH S mmm Layout 1 x ENE SUL AE E out solution xdmf D 5 Push Apply Information Abply ee Properties Reset Delete Search Properties Calculator Attribute Mode point Data 2 Result Array Name g r magnetic_field coords mag coords Clear t E Hat jHat kHat sin cos an abs sot asin acos atan ceil floor sinh cosh tanh xay exp vlv2 mag norm In log10 I Scalars v Vectors Display UnstructuredGridRepresentation Renresentation e r al x p Figure 12 File open window for ParaView Figure 13 Visualization of radial magnetic field by Paraview 60 References 1 Bullard E C and Gellman H Homogeneous dynamos and terrestrial magnetism Proc of the Roy Soc of London A247 213 278 1954 2 Christensen U R Aubert J Cardin P Dormy E Gibbons S Glatzmaier G A Grote E Honkura H Jones C Kono M Matsushima M Sakuraba
54. free The precise terms and conditions for copying distribution and modification fol low TERMS AND CONDITIONS Definitions This License refers to version 3 of the GNU General Public License Copyright also means copyright like laws that apply to other kinds of works such as semiconductor masks The Program refers to any copyrightable work licensed under this License Each licensee is addressed as you Licensees and recipients may be individuals or organizations To modify a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission other than the making of an exact copy The result ing work is called a modified version of the earlier work or a work based on the earlier work 80 A covered work means either the unmodified Program or a work based on the Program To propagate a work means to do anything with it that without permission would make you directly or secondarily liable for infringement under applicable copyright law except executing it on a computer or modifying a private copy Propagation includes copying distribution with or without modification making available to the public and in some countries other activities as well To convey a work means any kind of propagation that enables other parties to make or receive copies Mere interaction with a user through a computer network with no tr
55. g CMake on Mac OS X is the following ed work h5pfc show mpif90 I home matsui local include L home matsui local lib home matsui local lib libhdf5hl_fortran a home matsui local lib libhdf5_hl a home matsui local lib libhdf5_fortran a home matsui local lib libhdf5 a L home matsui local lib lmpi 1z ldl lm cmake DCMAKE LIBRARY PATH home matsui local lib DCMAKE INCLUDE PATH home matsui local include DHDF5 INCLUDE DIRS home matsui local include DHDF5 LIBRARY DIRS home matsui local lib DHDF5 LIBRARIES home matsui local lib libhdf5hl fortran a home matsui local lib libhdf5_hl a A home matsui local lib libhdf5 fortran a home matsui local lib libhdf5 a oA oo oe VO VY RR Vy After configuration compile and install are started by make make install 23 After running make command execute files are builtin CALYPSO HOME work bin directory 7 Simulation procedure Calypso consists of programs shown in Table 1 Because the serial programs do not use Table 1 List of program and required control file name Program Control file name Type gen_sph_grids control_sph_shell Serial sph_mhd control_MHD Parallel sph_initial_field control_MHD Parallel sph_add_initial_field control_MHD Parallel sph_snapshot control_snap
56. haracter is recognized as an end of character valuable if text with e g file prefix including file paths is not enclosed by or e Calypso s control file input is limited to 255 characters for each line 8 Examples Several examples are provided in the examples directory There are three subdirecto ries as examples README files are also provided to perform these examples in each subdirectory assemble_sph Examples for assembling program of spectrum data see section 11 dynamo benchmark Examples for dynamo benchmark by Christensen et al 2001 spherical shell Examples for preprocessing program see Section 9 8 1 Examples for preprocessing program Four examples illustrate the use of the preprocessing program The examples include Chebyshev points Example to generate indexing data using Chebyshev collocation points equidistance Example to generate indexing data with equi distance grid explicitly_defined Example to generate indexing data with explicitly defined ra dial points 26 begin spherical shell ctl begin data files def num subdomain ctl 4 sph file prefix sph shell in end data files def begin num grid sph truncation level ctl 4 ngrid meridonal ctl 12 grid zonal ctl 24 radial grid type ctl explicit array r layer 4 r layer 1 0 5384615384615 r_layer 2 0 5384615384615 r_layer 3 1 038461538462 4 a r_layer 1 538461538462 end array r_layer
57. he same as the volume spectrum data but radial grid point and radius of the layer is added in the list The following files are generated layer_pwr_prefix _1 dat Surface average of mean square amplitude of the fields as a function of spherical harmonic degree I and radial grid id k For scalar field the spectrum is fl LS fumtas m l 46 For vector field spectrum for the poloidal and toroidal components are written by mal 1 m Baak 7 gt BS as l meal 1 Brsg k I a BEY as layer_pwr_prefix _m dat Surace average of mean square amplitude of the fields as a function of spherical harmonic order m and radial grid id k The zonal wave number is referred in this spectrum data For scalar field the spectrum is 2 aney as For vector field spectrum for the poloidal and toroidal components are written by L P fsy k m l m Bss k m 3 f Bay Bg as Bleke gt I BA By as T 3 layer pwr prefix lm dat Surface average of mean square amplitude of the fields as a function of spherical harmonic order n I m and radial grid id k The wave number in the latitude direction is referred in this spectrum data For scalar field the spectrum is nen 35 f 0 Ed For vector field spectrum for the poloidal and toroidal components are written by l L Bouker SD f BEV Ba as prats 358 er Bas 10 6 Gauss coefficient data gauss coef prefix dat This program outpu
58. ication Distributed VTK ParaView http www paraview org Merged VTK ParaView Vislt https wci llnl gov codes visit Mayavi http mayavi sourceforge net XDMF ParaView Vislt e Disadvantage Many data files are generated Total data file size is large Only ParaView supports this format Distributed VTK data consist files listed in Table 5 For ParaView all subdomain data is read by choosing f1d_prefix step pvtk in file menu Table 5 List of written files for distributed VTK format name fld prefix step domain vtk VTK data for each subdomain fld_prefix step pvtk Subdomain file list for Paraview 10 4 2 Merged VTK data Merged VTK data have the following advantage and disadvantages to use e Advantage Merged field data is generated No external library is required Many applications support VTK format e Disadvantage 42 Very slow to output Total data file size is large Merged VTK data generate files listed in Table 6 Table 6 List of written files for merged VTK format name fld prefix stept vtk Merged VTK data 10 4 3 Merged XDMF data Merged XDMF data have the following advantage and disadvantages to use e Advantage Fastest output Merged field data is generated File size is smaller than the VTK formats e Disadvantage Parallel HDF5 library should be requir
59. il coef imp v ctl COEF INP U coef imp t ctl COEF INP T coef imp b ctl COEF INP B coef imp c ctl COEF INP C Detail x FFT library ctl FFT Name Detail Legendre trans loop ctl Leg Loop Detail e sph_monitor_ct1 Detail volume average prefix vol ave prefix Dp tail volume pwr spectr prefix vol pwr prefix Dp tail layered pwr spectr prefix layer pwr prefix Detail 38 picked sph prefix picked_sph_prefix Detail gauss coefs prefix gauss coef prefix Detail gauss coefs radius ctl qgauss coef radius Detail array pick layer ct Layer Detail array pick sph spectr ctl Degree Order Detail array pick sph degree ctl Degree Detail array pick sph order ctl Order Detail array pick gauss coefs ctl Degree Order Detail array pick gauss coef degree ctl Degree Detail array pick gauss coef order ctl Order Detail nphi mid eq ctl Nphi mid equator Detail 10 2 Spectrum data for restarting Spectrum data is used for restarting data and generating field data by Data transform pro gram sph snapshot sph zm snapshot or sph dynamobench This file is saved for each subdomain MPI processes then step and domain are added in the file name The step is calculated by time step ISTEP_RESTART 10 3 Thermal and compositional boundary condition data file Thermal and compositional heter
60. ility that these contractual assumptions directly impose on those licensors and authors All other non permissive additional terms are considered further restrictions within the meaning of section 10 If the Program as you received it or any part of it con tains a notice stating that it is governed by this License along with a term that is a further restriction you may remove that term If a license document contains a further restriction but permits relicensing or conveying under this License you may add to a covered work material governed by the terms of that license document provided that the further restriction does not survive such relicensing or conveying If you add terms to a covered work in accord with this section you must place in the relevant source files a statement of the additional terms that apply to those files or a notice indicating where to find the applicable terms Additional terms permissive or non permissive may be stated in the form of a sep arately written license or stated as exceptions the above requirements apply either way Termination You may not propagate or modify a covered work except as expressly provided under this License Any attempt otherwise to propagate or modify it is void and will automatically terminate your rights under this License including any patent licenses granted under the third paragraph of section 11 However if you cease all violation of this License then your li
61. in Value by real These name of the dimensionless numbers are used to construct coefficients for each terms in governing equations The following names can not be used because of reserved name in the program Table 16 List of reserved name of dimensionless numbers label field name value Zero zero 0 0 One one 1 0 Two two 2 0 Radial 35 Ratio of outer core thickness to whole core 0 65 1 0 35 67 AT coefficients_ctl Coefficients of each term in governing equations are defined in this block Each co efficients are defined by list of name of dimensionless number Name and its power Power For example coefficient for Coriolis term for the dynamo benchmark 2F l ig defined as array coef_4 Coriolis_ctl 2 coef 4 Coriolis ct Two 1 0 coef 4 Coriolis ct Ekman number 1 0 end array coef 4 Coriolis ctl Back to control MHD A 7 1 thermal Coefficients of each term in heat equation are defined in this block Back to control MHD coef 4 termal ctl Name Power T Coefficient for evolution of temperature DE and advection of heat u V T is defined by this array coef 4 t diffuse ctl Name Power Coefficient for thermal diffusion kj V T is defined by this array coef_4_heat_source_ctll Name Power Coefficient for heat source qr is defined by this array A 7 2 momentum Coefficients of each term in momentum equation are defined in this block Back to control
62. ligate you to collect a royalty for further conveying from those to whom you convey the Program the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program Use with the GNU Affero General Public License Notwithstanding any other provision of this License you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work and to convey the resulting work The terms of this License will continue to apply to the part which is the cov ered work but the special requirements of the GNU Affero General Public License section 13 concerning interaction through a network will apply to the combination as such Revised Versions of this License The Free Software Foundation may publish revised and or new versions of the GNU General Public License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns Each version is given a distinguishing version number If the Program specifies that a certain numbered version of the GNU General Public License or any later ver sion applies to it you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation If the Program does not specify a version number of the GNU General
63. ly Crank Nicolson scheme is only avail able for diffusion terms Crank Nicolson Crank Nicolson scheme for diffusion terms and second order Adams Bashforth scheme the other terms coef_imp_v_ctl COEF_INP_U Coefficients for the implicit parts of the Crank Nicolson scheme for viscous diffusion COEF_INP_U is defined by real coef_imp_t_ctl COEF_INP_T Coefficients for the implicit parts of the Crank Nicolson scheme for thermal diffusion COEF_INP_T is defined by real coef_imp_b_ctl COEF INP B Coefficients for the implicit parts of the Crank Nicolson scheme for magnetic diffusion COEF INP B is defined by real coef imp cctl COEF INP C Coefficients for the implicit parts of the Crank Nicolson scheme for compositional diffu sion COEF INP C is defined by real FFT library ctl FFT Name FFT library name for Fourier transform is defined by text The following libraries are available for FFT Name If this flag is not defined program searches the fastest library in the initialization process FFTW Use FFTW FFTPACK Use FFTPACK FFT library ctl FFT Name Loop configuration for Legendre transform is defined by text The following settings are available for Leg Loop If this flag is not defined program searches the fastest approarch in the initialization process Inner radial loop Loop for the radial grids is set as the innermost loop 73 Outer radial loop Loop for the radi
64. mission to run the unmodified Program The output from running a covered work is covered by this License only if the output given its content constitutes a covered work This License acknowledges your rights of fair use or other equivalent as provided by copyright law You may make run and propagate covered works that you do not convey without conditions so long as your license otherwise remains in force You may convey covered works to others for the sole purpose of having them make modifications exclusively for you or provide you with facilities for running those works provided that you comply with the terms of this License in conveying all material for which you do not control copyright Those thus making or running the covered works for you must do so exclusively on your behalf under your direction and control on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you Conveying under any other circumstances is permitted solely under the conditions stated below Sublicensing is not allowed section 10 makes it unnecessary Protecting Users Legal Rights From Anti Circumvention Law No covered work shall be deemed part of an effective technological measure un der any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996 or similar laws prohibiting or restricting cir cumvention of such measures 82 When you convey
65. nction of order m is written in layer pwr prefix m dat and spectrum as a function of I m is written in layer pwr prefix lm dat If this file prefix is not defined sphere averaged spectrum data are not generated picked sph prefix picked sph prefix File prefix for picked spectrum data picked sph prefix is defined by Text Pro gram add dat extension after this file prefix If this file prefix is not defined picked spectrum data are not generated 74 gauss coefs prefix gauss coef prefix File prefix for Gauss coefficients gauss coef prefix is defined by Text Program add dat extension after this file prefix If this file prefix is not defined Gauss coefficients data are not generated gauss coefs radius ctl gauss_coef_radius Normalized radius to obtain Gauss coefficients gauss_coef_radius is defined by real Gauss coefficients are evaluated from the poloidal magnetic field at CMB by as suming electrically insulated mantle Do not set gauss_coef_radius less than the outer core radius ro array pick layer ctl Layer Listof radial grid point number Layer to output spectrum data by integer If this array is not defined picked spectrum data are written for all radial grid points array pick sph spectr ctl Degree Order List of spherical harmonics mode I and m of spectrum data to output Degree and Order are defined by integer array pick sph degree ctl Degree Degrees l
66. ndi tions for poloidal and toroidal coefficients are described as van St o Uri r ei UR Oz Ure r ror and DEN Oforl gt 2 12 5 4 4 Fixed homogenous temperature When a constant temperature T is is applied the spherical harmonic coefficients are Tor Ts and T r Oforl gt 1 5 4 5 Fixed homogenous heat flux A constant heat flux is imposed by setting the radial temperature gradient to Fr The spherical harmonic coefficients are OT zn 33 gt ei r Tb and A Oforl gt 1 Or 5 4 6 Fixed composition When a constant composition C is applied the spherical harmonic coefficients are Colr Ch and Or Oforl gt 1 5 4 7 Fixed composition flux A constant composition flux is imposed by setting the radial composition gradient to Fo The spherical harmonic coefficients are ace Ee a Tr Cb and ie 0 ford gt 1 Or 13 5 4 8 Connection to the magnetic potential field If the regions outside the fluid shell are assumed to be electrical insulators current density vanishes in the electric insulator y ext 0 where the suffix ext indicates fields outside of the fluid shell At the boundaries of the fluid shell the magnetic field B ftuia current density J fluia and electric field E ftuia in the conductive fluid satisfy B ptuia a Beet 0 J fluid ER Ja TE 0 and E fluid Eext x f 0 where 7 is the radial unit vector i e normal vector for the spheri
67. nvection was added to the FEM dynamo model by Hiroaki Matsui in 2009 Progress in understanding the role of subgrid scale models in magnetohydrodynamic simulations relies on quantitative estimates for the transfer of energy between spatial scales This information is most easily obtained from a spherical harmonic expansion of the simulation results even when the simulation is performed by FEM Hiroaki Matsui implemented the spherical harmonic transform in 2007 using a combination of MPI and 5 OpenMP and later included the spherical harmonic transform routines into his old dynamo code to create Calypso Additional software in the program package for visualization is based on data formats from the FEM model In addition the control parameter file format 1s adapted from the input formats used in GeoFEM Currently Calypso Ver 1 0 supports the following features and capabilities 2 1 Magnetohydrodynamics simulation for a Boussinesq fluid in a rotating spherical shell Convection driven by thermal and compositional buoyancy Temperature or heat flux is fixed at boundaries Composition or compositional flux is fixed at boundaries Non slip or free slip boundary conditions Outside of the fluid shell is electrically insulated or pseudo vacuum boundary A conductive inner core with the same conductivity as the surrounding fluid A rotating inner core driven by the magnetic and viscous torques Updates for Ver 1 1 In Version 1 1 a number of
68. o described by using the poloidal and toroidal coef ficients as OBS Or Brr r Water r fo 15 6 Installation 6 1 Library Requirements Calypso requires the following libraries e GNU make e MPI libraries OpenMPI MPICH etc e FFTPACK Ver 5 1D http people sc fsu edu jburkardt f_src fftpack5 1d fftpack5 1d html The source files for FFTPACK are in cluded in src EXTERNAL_1ibs directory Linux and Max OS X use GNU make as a default make command but some system e g BSD or SOLARIS does not use GNU make as default configure command searches and set correct GNU make command In addition the following libraries can be used optional e OpenMP e FFTW version 3 http www fftw org including Fortran wrapper e PARALLEL HDF5 http www hdfgroup org HDF5 PHDF5 including Fortran wrapper Note Calypso does NOT use MPI and OpenMP features in FFTW3 In the most of platforms the Fourier transform is faster than that by FFTPACK HDES is used for field data output with XDMF format instead of VTK format The comparison of field data format is described in section refsec VTK OpenMP is used for the parallelization under the shared memory Better choice to use both MPI and OpenMP parallelization so called Hybrid parallelization or only using MPI so called flat MPI is depends on the computational platform and compiler For example flat MPI has much better performance on Linux cluster with Intel Xeon
69. ogeneity at boundaries are defined by a external file named boundary data name In this file temperature composition heat flux or compositional flux at ICB or CMB can be defined by spherical harmonics coeffi cients To use boundary conditions in boundary data name file name is de fined by boundary data file name column in control file and boundary condition type type is setto fixed fileorfixed flux fileinbc temperature or be composition column By setting fixed fileorfixed flux file in con trol file boundary conditions are copied from the file boundary data name 39 An example of the boundary condition file is shown in Figure 6 As for the control file a line starting from or is recognized as a comment line In boundary data name boundary condition data is defined as following 1 Number of total boundary conditions to be defined in this file 2 Field name to define the first boundary condition 3 Place to define the first boundary condition LCB or CMB 4 Number of spherical harmonics modes for each boundary condition 5 Spectrum data for the boundary conditions degree order m and harmonics coef ficients 6 After finishing the list of spectrum data return to Step 2 for the next boundary con dition If harmonics coefficients of the boundary conditions are not listed in item 5 0 0 is au tomatically applied for the harmonics coefficients of the boundary conditions So only non zero com
70. or vector field spectrum for the poloidal and toroidal components are written by Baud p f Bay ay m l 1 m l Bral gt BR dv ol If the vector field F is not solenoidal i e V F 4 0 The poloidal component of mean square data are included mean square field of the potential components as Feall 7 Y f BEP CVOR av m 1 vol pwrprefix m dat Volume average of mean square amplitude of the fields as a function of spherical harmonic order m The zonal wave number is referred in this spectrum data For scalar field the spectrum is faen EE f errar 45 For vector field spectrum for the poloidal and toroidal components are written by 1 l m E Baum FY 182 Bar av Bram 7 f BRP 857 av vol pwr prefix _lm dat Volume average of mean square amplitude of the fields as a function of spherical harmonic order n l m The wave number in the latitude direction is referred in this spectrum data For scalar field the spectrum is fan flo fi Gr dv For vector field spectrum for the poloidal and toroidal components are written by les Tie lt LT DM n Bgsq n Brsg n Sie n 10 5 3 layered spectrum data Spectrum data for the each radial position are written by defining volume_pwr_spectr_prefix in control file By defining layered pwr_spectr prefix following spectrum data averaged over the fluid shell is written Data format is t
71. orthogonality relation for the spherical harmonics is f YY sin0ddp 4 is 1 TM Aol ad where w is Kronecker delta 5 3 Evaluation of Coriolis term The curl of the Coriolis force 2QV x 2 x u is evaluated in the spectrum space using the triple products of the spherical harmonics These 3j symbols or Gaunt integral Guam 1 and Elsasser integral EM are written as gumm f YM YPY sin 0d0d OV OYE NTN YM AO dodo cae ap ad a The Gaunt integral 1 47 G Mp and Elsasser integral 1 47 EM for the Coriolis terms are evaluated in the simulation program Mmm Erm 11 5 4 Boundary conditions Calypso currently supports the following boundary conditions for velocity u magnetic field B temperature T and composition variation C These boundary conditions are defined in the control file control MHD 5 4 1 Non slip boundary The velocity u is set to be O at the boundary For poloidal and toroidal coefficients of velocity Ug r and U77 r the boundary condition can be described as OU gi Usi r gt Or 0 and bre 5 4 2 Free slip boundary For a free slip boundary shear stress and radial flow vanish at the boundary The boundary condition for poloidal and toroidal coefficients are described as us 55 unm 0 fl om 5 50 0 and 5 4 3 Fixed rotation rate If the boundary rotates with a rotation vector 2 Qbr Qoy Qoz the boundary co
72. ponents need to be listed in the boundary condition file 10 4 Field data for visualization Field data is used for the visualization processes Field data are written with XDMF format http www xdmf org index php Main Page merged VTK or distributed VTK format http www vtk org VIK img file formats pdaf The out put data format is defined by f1d format Visualization applications which we checked are listed in Table Because the field data is written by using Cartesian coordinate x y z system coordinate conversion is required to plot vector field in spherical coor dinate r 0 4 or cylindrical coordinate s d z We will introduce a example of visual ization process using ParaView in Section 17 10 4 1 Distributed VTK data Distributed VTK data have the following advantage and disadvantages to use e Advantage Faster output No external library is required 40 se He number of boundary conditions 4 boundary condition data list it it it it Fixed temperature at ICB temperature ICB 000 1 0E 00 t 2 0E 01 2 2 3 0E 01 ij Fixed heat flux at CMB heat_flux CMB 2 0 0 0 9E 0 1 1 5 0E 1 Fixed composition flux at ICB composite_flux ICB 0 0 0 0E 00 2 0 2 5E 01 ij Fixed composition at CMB composition CMB 2 0 0 1 0E 00 2 2 5 0E 01 Figure 6 An example of boundary condition file 41 Table 4 Checked visualization application Format Appl
73. processors and with Intel fortran compiler but Hybrid model has better performance on Hitachi SR16000 with Power 6 processors 6 2 Known problems FFTPACK and Intel compiler FFTPACK fails to compile with Intel fortran using the warn all option Currently the warn all option is excluded by Makefile when FFTPACK is compiled 16 Homebrew s FFTW3 on Mac OS X Calypso uses Fortran wrappers in FFTW3 If FFTW3 is installed using Homebrew for Mac OS X http mxcl github com homebrew the required fortran wrappers are not installed In this case please install FFTW3 with Fortran wrappers with another pack age manager Macports for example build FFTW3 by yourself including the Fortran wrapper or turn off FFTW3 features in Calypso Cross compiler support configure command in Calypso does not support cross compilation If you want to compile with a cross compiler please set the variables in Makefile manually see section 6 3 Directories The top directory of Calypso ex CALYPSO_ HOME contains the following directories ed CALYPSO HOME ls CMakeLists txt Makefile in configure in examples INSTALL bin doc src LICENSE configure doxygen work A oo bin directory for executable files cmake directory for cmake configurations cmake directory for document generated by doxygen doc documentations examples examples src source files work work directory Compile is done in this directory
74. ption remove any additional permissions from that copy or from any part of it Additional permis sions may be written to require their own removal in certain cases when you modify the work You may place additional permissions on material added by you to a covered work for which you have or can give appropriate copyright permission Notwithstanding any other provision of this License for material you add to a cov ered work you may if authorized by the copyright holders of that material supple ment the terms of this License with terms a Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License or b Requiring preservation of specified reasonable legal notices or author attribu tions in that material or in the Appropriate Legal Notices displayed by works containing it or c Prohibiting misrepresentation of the origin of that material or requiring that modified versions of such material be marked in reasonable ways as different from the original version or d Limiting the use for publicity purposes of names of licensors or authors of the material or e Declining to grant rights under trademark law for use of some trade names trademarks or service marks or 86 f Requiring indemnification of licensors and authors of that material by any one who conveys the material or modified versions of it with contractual assumptions of liability to the recipient for any liab
75. quivalent access to the Corresponding Source in the same way through the same place at no further charge You need not require recipients to copy the Corresponding Source along with the object code If the place to copy the object code is a network server the Corresponding Source may be on a different server operated by you or a third party that supports equivalent copying facilities provided you maintain clear directions next to the object code saying where to find the Corresponding Source Regardless of 84 what server hosts the Corresponding Source you remain obligated to ensure that it is available for as long as needed to satisfy these requirements e Convey the object code using peer to peer transmission provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d A separable portion of the object code whose source code is excluded from the Corresponding Source as a System Library need not be included in conveying the object code work A User Product is either 1 a consumer product which means any tangible per sonal property which is normally used for personal family or household purposes or 2 anything designed or sold for incorporation into a dwelling In determining whether a product is a consumer product doubtful cases shall be resolved in favor of coverage For a particular product received by a particula
76. r user normally used refers to a typical or common use of that class of product regardless of the status of the particular user or of the way in which the particular user actually uses or expects or is expected to use the product A product is a consumer product regardless of whether the product has substantial commercial industrial or non consumer uses unless such uses represent the only significant mode of use of the product Installation Information for a User Product means any methods procedures au thorization keys or other information required to install and execute modified ver sions of a covered work in that User Product from a modified version of its Corre sponding Source The information must suffice to ensure that the continued func tioning of the modified object code is in no case prevented or interfered with solely because modification has been made If you convey an object code work under this section in or with or specifically for use in a User Product and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term regardless of how the transaction is characterized the Corresponding Source conveyed under this section must be accompanied by the Installation Information But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the U
77. rgy KE total Total kinetic energy ME pol Poloidal magnetic energy Case I and 2 ME tor Toroidal magnetic energy Case 1 and 2 ME total Total magnetic energy Case I and 2 ME pol ic Poloidal magnetic energy in inner core Case 2 ME tor icore Toroidal magnetic energy in inner core Case 2 ME totalicore Total magnetic energy in inner core Case 2 omega icz Angular velocity of inner core rotation Case 2 MAG torque ic z Magnetic torque integrated over the inner core Case 2 phi l 4 Longitude where u 0 and Ou 0O gt 0 at mid depth in equatorial plane omega vp44 Drift frequency evaluated by V component omega_vt54 Drift frequency evaluated by V component B theta component of magnetic field at requested point vphi component of velocity at requested point 55 temp Temperature at requested point t_step time KE_pol KE_tor KE_total ME_pol ME_t or ME_total ME_pol_icore ME_tor_icore ME omega_ic_z MAG_torque_ic_z phi I phi 2 phi 4 omega vp44 omega vt54 B theta v phi 20000 9 999999999998981E 001 1 5340597320730 431439471284618E 001 3 965499203357688E 001 2 40 09E 000 1 648662987055900E 000 4 054356999010911E 8687924452961E 001 4 812865754441352E 001 3 95681 total_icore phi_3 temp 72E 00 5694011955 000 S69 6581997376E N El OD 8 001 5 220517005592486E 000 2 321885847438682E 002 3 59417 562666330
78. rm under the terms of sections 4 and 5 provided that you also convey the machine readable Corresponding Source under the terms of this License in one of these ways a Convey the object code in or embodied in a physical product including a physical distribution medium accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange b XX Convey the object code in or embodied in a physical product including a physical distribution medium accompanied by a written offer valid for at least three years and valid for as long as you offer spare parts or customer support for that product model to give anyone who possesses the object code either 1 a copy of the Corresponding Source for all the software in the product that is covered by this License on a durable physical medium customarily used for software interchange for a price no more than your reasonable cost of physically performing this conveying of source or 2 access to copy the Corresponding Source from a network server at no charge c Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source This alternative is allowed only occasion ally and noncommercially and only if you received the object code with such an offer in accord with subsection 6b d ww Convey the object code by offering access from a designated place gratis or for a charge and offer e
79. rocessing program gen sph grid Input data Program Output data Parallel Spectr index data FEM mesh data Figure 4 Generated files by preprocessing program in Data flow This program generates index table and a communication table for parallel spherical harmonics table of integrals for Coriolis term and FEM mesh information to generate visualization data see Figure 14 This program needs control file for input The output files include the indexing tables Table 2 List of files for gen sph grid extension Parallelization I O control sph grid Single Input sph prefix domaint rj Distributed Output sph prefix domainff rlm Distributed Output sph prefix domainf rtm Distributed Output sph prefix domainf rtp Distributed Output sph prefix domainf gfm Distributed Output radial info dat Single Output 9 1 Position of radial grid The preprocessing program sets the radial grid spacing either by a list in the control file or by setting an equidistant grid or Chebyshev collocation points 30 In equidistance grid radial grids are defined by k k r k ri r r eo where krop is the grid points number at ICB The radial grid set from the closest points of minimum radius defined by Min radius ct1l in control file to the closest points of the maximum radius defined by Max radius ct1 fin control file and radial grid number for the innermos
80. ry condition data file boundary data name is optionally required if boundary conditions for temperature and composition are not homogenious 34 Table 3 List of files for simulation sph_mh name Parallelization I O control MHD Serial Input sph prefix domainf rj Distributed Input sph prefix domainf rim Distributed Input sph prefix domainf rtm Distributed Input sph prefix domaintf rtp Distributed Input sph prefix domain gfm Distributed Input boundary data name Single Input rst prefix stepf domainf fst Distributed Input Output vol_pwr_prefix dat Single Output vol pwr prefix l dat Single Output vol pwr prefix m dat Single Output vol pwr prefix lm dat Single Output vol ave prefix dat Single Output layer pwr prefix 1l dat Single Output layer pwr prefix m dat Single Output layer pwr prefix lm dat Single Output gauss coef prefix dat Single Output picked sph prefix dat Single Output f1d_prefix step domain extension Output 35 10 1 Control file The format of the control file control MHI is described in section You can jump to detailed description by clicking Detail MH D_control Header of the control file e data files def Detail num subdomain ctl num smp ctl sph file prefix boundary data file name tail restart file
81. ser Product for example the work has been installed in ROM The requirement to provide Installation Information does not include a requirement to continue to provide support service warranty or updates for a work that has been modified or installed by the recipient or for the User Product in which it has been modified or installed Access to a network may be denied when the modification 85 itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network Corresponding Source conveyed and Installation Information provided in accord with this section must be in a format that is publicly documented and with an imple mentation available to the public in source code form and must require no special password or key for unpacking reading or copying Additional Terms Additional permissions are terms that supplement the terms of this License by making exceptions from one or more of its conditions Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License to the extent that they are valid under applicable law If additional permissions apply only to part of the Program that part may be used separately under those permissions but the entire Program remains governed by this License without regard to the additional permissions When you convey a copy of a covered work you may at your o
82. shot Parallel sph_dynamobench control_snapshot Parallel sph_zm_snapshot control_snapshot Parallel assemble_sph control_sph_assemble Serial MPI they are simply invoked by program Parallel programs must be invoked using MPI commands On a Linux cluster using MPICH parallel programs are invoked with mpirun np of processes program This command will vary depending on the MPI implementation installed on the ma chine Please consult with your sysadmin for details To perform simulations by Calypso the following processes are required 1 Generate grids and spherical harmonics indexing information by gen_sph_grids 2 Make initial fields by sph initial field if necessary 3 Perform the simulation by sph_mhd 24 4 Convert the parallel spectra data by assemble_sph to continue with changing number of processes if necessary 5 Data analysis by sph snapshot sph snapshot or sph_dynamobench 6 Update initial fields by sph add initial field for more simulations if nec essary The simulation program sph mhd requires an indexing file for spherical transform sph_mhd generates spectrum data and monitoring data and field data in Cartesian coordinate as outputs The data transform programs sph snapshot and sph zm snapshot generate outputs data from parallel spectra data The flow of data is shown in Figure 2 Input data Program Output data Spectr data Snapshots data Parallel Spec
83. sition and compositional flux and permits a conductive and rotatable inner core Results are written as spherical harmonics coefficients Gauss coefficients for the re gion outside of the fluid shell and field data in Cartesian coordinate for easily visualization with a number of visualization programs This user guide describes the essentials of the magnetohydrodynamics theory and equations behind Calypso and provides instructions for the configuration and execution of Calypso 2 History Calypso has its origins in two earlier projects One is a dynamo simulation code written by Hiroaki Matsui in 1990 s using a spectral method This code solves for the poloidal and toroidal spectral coefficients like Calypso but it calculates the nonlinear terms in the spectral domain using a parallelization for SMP architectures The other project is the thermal convection version of GeoFEM which is Finite Element Method FEM platform for massively parallel computational environment originally written by Hiroshi Okuda in 2000 Hiroaki Matsui was responsible for adding routines to GeoFEM to perform magneto hydrodynamics simulation in a rotating frame In 2002 this code successfully performed dynamo simulations in a rotating spherical shell using insulating magnetic boundary con ditions The following year Matsui implemented a subgrid scale SGS model in the FEM dynamo model in collaboration with Bruce Buffett A module to solve for double diffusive co
84. ssary For more information on this and how to apply and follow the GNU GPL see http www gnu org licenses The GNU General Public License does not permit incorporating your program into proprietary programs If your program is a subroutine library you may consider it more useful to permit linking proprietary applications with the library If this is what you want to do use the GNU Lesser General Public License instead of this License But first please read http www gnu org philosophy why not 1gp1 html 93
85. st of field name for time evolution label field name Description velocity Velocity u temperature Temperature T composition Composition variation C magnetic field Magnetic field B array bc temperature Group Type Value Boundary conditions for temperature are defined by this array Position of boundary is defined in Group column by ICB or CMB The following type of boundary conditions are available for temperature in Type column fixed Fixed homogeneous temperature on the boundary The fixed value is defined in Value by real fixed file Fixed temperature defined by external file Value in this line is ig nored See section 10 3 fixed flux Fixed homogeneous heat flux on the boundary The value is defined in Value by real Positive value indicates outward flux from fluid shell e g Flux to center at ICB and Flux to mantle at CMB are positive fixed flux file Fixed heat flux defined by external file Value in this line is ignored See section array bcvelocity Group Type Value Boundary conditions for velocity are defined by this array Position of boundary is defined in Group by ICB or CMB The following boundary conditions are available for velocity in Type column non slip sph Non slip boundary is applied to the boundary defined in Group Real value is required in Value but they value is not used in the program free slip sph Free slip boundary is applied to the boundary de
86. stensen et al The following files are used for this program Table 11 List of files for dynamo benchmark check sph_dynamobench name Parallelization VO control_snapshot Serial Input sph prefix domain rj Distributed Input sph prefix domain rlm Distributed Input sph prefix domaint rtm Distributed Input sph prefix domain rtp Distributed Input rst_prefix step domain fst Distributed Input dynamobench dat Single Output 14 1 Dynamo benchmark data dynamobench dat In benchmark test by Christensen et al both global values and local values are checked 1 f1 As global results Kinetic energy V su dV in the fluid shell magnetic energy in 1 1 1 the fluid shell 2B dV for case 1 and 2 and magnetic energy in the solid VEPmJ 2 54 1 1 1 inner sphere V EPm a 5B dv for case 2 only Benchmark also requests By in i m creasing number of grid point at mid dpeth of the fluid shell in the equatorial plane by program can find accurate solution for the point where u 0 and Ou O gt 0 Angular frequency of the field pattern with respect to the direction is also required The benchmark test also requires temperature and 6 component of velocity In the text file dynamobench dat the following data are written in one line for every i step rst ctl step t_step Time step number time Time KE pol Poloidal kinetic energy KE tor Toroidal kinetic ene
87. t the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program to make sure it remains free software for all its users We the Free Software Foundation use the GNU General Public License for most of our software it applies also to any other work released this way by its authors You can apply it to your programs too When we speak of free software we are referring to freedom not price Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software and charge for them if you wish that you receive source code or can get it if you want it that you can change the software or use pieces of it in new free programs and that you know you can do these things To protect your rights we need to prevent others from denying you these rights or asking you to surrender the rights Therefore you have certain responsibilities if you distribute copies of the software or if you modify it responsibilities to respect the freedom of others For example if you distribute copies of such a program whether gratis or for a fee you must pass on to the recipients the same freedoms that you received You 79 must make sure that they too receive or can get the source code And you must show them these terms so they know their rights Developers that use the GNU GPL protect your rights with two steps 1 assert copyright on the software and 2 offer
88. t points is set to k 1 In Chebyshev collocation points radial grids in the fluid shell are defined by cy fl ano For the inner core r lt r grid points is defined by and grid points in the external of the shell r gt r is defined by Vs 1 k komp ri Tot gg z 608 Ty where komp is the grid point number at CMB 9 2 Control file control sph shell Control file control sph shell consists the following items Detailed description for each item can be checked by clicking Detail at the end of each item spherical_shell_ctl e data files def Detail num subdomain ctl Num PE Detail sph file prefix sph prefix Detail e num domain ctl Detail array num domain sph grid Direction Ndoma in Dp tail 31 array num domain legendre Direction Ndoma in Dp tail array num domain spectr Direction Ndoma in Dp tail e num grid sph Detail truncation level ctl ngrid meridonal ctl ngrid zonal ctl radial grid type ctl Detail num fluid grid ctl fluid core size ctl ICB to CMB ratio ctl Min radius ctl Max radius ctl array r layer array boundaries ctl tail 9 3 Spectrum index data Lmax Detail Ntheta Detail Nphi Detail explicit Chebyshev or equi_distance Nr shell Detail Length Detail R ratio Detail Rmin Detail Rmax
89. t selected Gauss coefficients of the magnetic field Gauss coefficients is evaluated for radius defined by gauss coef radius every increment monitor steps Gauss coefficients are evaluated by using poloidal magnetic field at CMB Bsr ro and radius defined by gauss_coef_radius reas m l Po m q 2 2 Bay ro m l To i m hj r2 2 By To The data file has the following headers in the first three lines line 2 Number of saved Gauss coefficients and reference radius line 3 Labels of Gauss coefficients data The data consists of time step time and Gauss coefficients for each step in one line If the Gauss coefficients data file exist before starting the simulation programs append Gauss coefficients at the end of files without checking constancy of the number of data and order of the field If you change the configuration of data output structure please move the old Gauss coefficients file to another directory before starting the programs 10 7 Spectrum monitor data picked_sph_prefix dat This program outputs spherical harmonics coefficients at specified spherical harmonics modes and radial points in single text file Spectrum data marked Monitor_On are written in our line for each spherical harmonics mode and radial point every increment_monitor steps If the spectrum monitor data file exist before starting the simulation programs append spectrum data at the end of files without checking con stancy of the number of
90. ta Please run it after taking a backup This program modifies or adds new data to an initial field file It could be used to start a new geodynamo simulation by adding seed magnetic field or source terms to a non magnetic convection simulation The initial fields to be added are also defined in const_sph_initial_spectr f90 data utilities INITIAL FIELD directory This program also needs the files listed in Table 10 This program generates the spectrum data files rst prefix step domain fst To use generated initial data file set ISTEP START and ISTEP RESTART to be appropriate time step and increment respectively To read the original initial field data INITIAL TYPE is set to befstart from rst filelin control MHD In other words the step in the file name ISTEP_START and ISTEP RESTART in the control file should be the consistent 53 Table 10 List of files for simulation sph add initial field name Parallelization VO control_MHD Serial Input sph prefix domainf rj Distributed Input sph prefix domainf rim Distributed Input sph prefix domainf rtm Distributed Input sph prefix domainf rtp Distributed Input rst prefix step domain fst Distributed Input Output 14 Check program for dynamo benchmark sph dynamobench This program is only used to check solution for dynamo benchmark by Chri
91. tional Packages with PACKA without PA GE ARG use PACKAGE ARG yes CKAGE do not use PACKAGE same as with PACKAGE no with hdf5 Some influenti oe I DD yes no PATH full path of h5pcc for parallel HDF5 configuration al environment variables CC CFLAGS LDFLAGS LIBS CPPFLAGS EC FCFLAGS MP ICC MP IFC PKG CONFIG CPP FFTW3 CFLAGS FFTW3 LIBS An example of C compiler command C compiler flags linker flags e g L lt lib dir gt if you have libraries in a nonstandard directory lt lib dir gt libraries to pass to the linker e g l lt library gt Objective C C preprocessor flags e g I lt include dir gt if you have headers in a nonstandard directory lt include dir gt Fortran compiler command Fortran compiler flags MPI C compiler command MPI Fortran compiler command path to pkg config utility C preprocessor C compiler flags for FFIW3 overriding pkg config linker flags for FFTW3 overriding pkg config usage of the configure command is the following configure prefix Users matsui local CFLAGS 0 Wall g FCFLAGS 0 Wall g PKG_CONFIG_PATH Users matsui local lib pkgconfig enable fftw3 with hdf5 Users matsui local bin h5pcc 6 5 2 Compile Compile is performed using the make command The Makefile in the top directory is used to generate another Makefile in the work
92. tions for composition variation are defined by this array Position of boundary is defined in Group by ICB or CMB The following boundary conditions are available for composition variation in Type column fixed Fixed homogeneous composition on the boundary The fixed value is defined in Value by real fixed file Fixed composition defined by external file Value in this line is 1g nored See section 10 3 fixed flux Fixed homogeneous compositional flux on the boundary The value is defined in Value by real Positive value indicates outward flux from fluid shell e g Flux to center at ICB and Flux to mantle at CMB are positive fixed flux file Fixed compositional flux defined by external file Value in this line is ignored See section 66 A 5 forces define Forces for the momentum equation are defined in this block Back to control MHD array force ctl Force Name of forces for momentum equation are listed in Force by text The following fields are available Table 15 List of force Label Field name Equation Coriolis Coriolis force 202 x u Lorentz Lorentz force JxB gravity Thermal buoyancy arT g Composite gravity Compositional buoyancy acCg A 6 dimensionlessctl Dimensionless numbers are defined in this block Back to control MHD array dimless_ctl Name Value Dimensionless are listed in this array The name is defined in Name by text and value is defined
93. tr index data Spectr data Initial field FEM mesh data Figure 2 Data flow of the simulation Simulations require index data for spherical har monics transform initial spectra optional data and FEM mesh data Simulation program also outputs spectra data monitoring data and field data in Cartesian coordinate Data transform program generates output data for simulation program from spectra data Field data VTK or XDMF Each program needs one control file the name of which is defined by the program Standard input is not supported by Fortran 90 so Calypso uses control files The appro priate control file names are shown in the Table 1 The following rules are used in the control files An example of a control file is shown in Figure 3 e Lines starting with or are treated as a comment lines and ignored e All control files consist of blocks which start with begin name and end with end name 25 e The item name is shown first and the associated value data is second e The order of items and blocks can be changed e If an item consists of multiple data these should be listed in one line e If an item does not belong in the block it is ignored e Anarray block starts with begin array name number of components and ends with end array name e If number of components for an array is 0 end array name on the next line is not needed e In Fortran program c
94. y you can use the programs in SRCDIR bin directory without running make install If directory S PREFIX does not exist make install creates PREFIX PREFIX lib PREFIX bin and S PREFIX include directories No files are installed in S PREFIX lib and S PREFIX include 20 6 6 Install without using configure It is possible to compile Calypso without using the configure command To do this you need to edit the Makefile First copy Makefile from template Makefile in as cp Makefile in Makefile In Makefile the following variables should be defined SHELL Name of shell command SRCDIR Directory of this Makefile NSTDIR Install directory MPICHDIR Directory names for MPI implementation If you set fortran90 compiler name for MPI programs in MP IF 90 you do not need to define this valuable MPICHINCDIR Directory names for include files for MPI implementation If you set fortran90 compiler name for MPI programs in MPIF 90 you do not need to define this valuable MPILIBS Library names for MPI implementation If you set fortran90 compiler name for MPI programs in MP IF 90 you do not need to define this valuable F90 LOCAL Command name of local Fortran 90 compiler to compile module depen dency listing program MPIF90 Command name of Fortran90 compiler and linker for MPI programs If com mand

User Manual Version 1.1 - Computational Infrastructure for

Contents

Download Pdf Manuals

Related Search

Related Contents