ICES User Manual - University of Michigan
Contents
1. 05 CG 3 0 au 06 CG 3 0 au 07 CG 3 0 au 08 CG 3 0 au 09 CG 3 0 au 10 CG 3 0 au 11 CG 3 0 au 12 CG 3 3 au 00 2d 2d 2d 2d 2d 2d 2d 2d 2d 2d 2d 2d 2d 2d 2d 1d 1d 1d 1d 1d 1d 2d CO Dust H20 CO Dust H20 CO Dust H20 CO 02 Dust CO C02 Dust CO 02 Dust CO 02 Dust CO C02 Dust CO 02 Dust CO 02 Dust CO C02 Dust CO C02 Dust CO 02 Dust CO C02 Dust CO C02 Dust C CO Dust C CO Dust C CO Dust C CO Dust C CO Dust C CO Dust CO Dust H20 Hio Hd Hd Hd Hio Hi H20 H20 H20 H20 H20 H20 H20 H20 H20 H20 H20 H20 H2 H2 H2 H2 H2 H2 the DSMC model Original ISSI Case V1 4 Original ISSI Case V1 4 Original ISSI Case V1 4 H20 Driven V1 4 H20 Driven V1 4 C0 C02 Driven V1 4 C0 C02 Driven V1 4 H20 Driven Jet V1 4 C0 C02 Driven Jet V1 4 H20 Driven V1 4 H20 Driven V1 4 C0 C02 Driven V1 4 CO C02 Driven V1 4 H20 Driven Jet V1 4 C0 C02 Driven Jet V1 4 OH H20 Driven V1 5 OH CO Driven V1 5 OH CG 3 0 au 07 with Q 204 V1 0 H20 OH CG_3 0_au_07 with Q 20 V1 0 H20 0 OH CG 3 0 au 07 with Q 504 V1 0 H20 0 OH CG 3 0 au 07 with Q 50 V1 0 Original ISSI Case V1 4 H20 H20 H20 extract data for modules you use ICES c pl with 4 arguments in command line The command we use to carry out the test make test is ICES_c pl Tests traj_xaxi2. 29 4 2 Using your unlisted compiler 2 res 29 acp MEET 30 4 3 1 MHD Unable to read from opened MHD 30 IM 30 4 3 3 Errors when running make 30 O PPP 30 4 CONTENTS 5 Available Cases for the Coma 33 5 1 67P Churvumov Gerasimenko 33 6 Available Cases for the Nucleus 37 7 Physic Module Details 39 Sh ists Gini ek GOR et ee ho ead eee oe Ge es ees 39 SE Ree KS ee ee 40 3 Blectronsih e a ich ioo Wo sleden a she Xe SR ee Mark ek GAAR Eee piros eed us 40 41 Chapter 1 Introduction This document describes the Inner Coma Environment Simulation tools ICES The tool development began with the efforts of our ISSI comet modeling team and have continued as a part of our work with the ESA Rosetta mission Out original intent was provide the comet community with access to results from a comprehensive set of models of the cometary coma ranging from the surface out to the interaction with the solar wind and covering dust gas and plasma phases We have now expanded the tool to include nucleus models Our initial target comet is 67P Churyumov Gerasimenko with specific application to the Rosetta mission Our intent is that the tool will be useful for mission and science planning as well as for data interpretation The ICES tool does not run the individual models but rather extracts
3. Depth Flag Temperature Mass Density Porosity Pore size Amorphous Ice MF Crystalline Ice MF Permanent dust MF Dust lum MF Dust 10um MF Dust 100um MF Dust 200um MF Water flux lum dust flux 10um dust flux 100um dust flux 200um dust flux Valid Depth All All All All All All Sub surface Sub surface Sub surface Sub surface Sub surface Sub surface Sub surface Sub surface Sub surface Sub surface Surface Surface Surface Surface Surface 27 Unit deg deg K Kg m Kg sec m Kg sec 2 Kg sec m Kg sec m 28 CHAPTER 3 INPUT AND OUTPUT FILES Chapter 4 Troubleshooting 4 1 Installing compilers The free GNU Fortran compiler gfortran can be downloaded from http gcc gnu org wiki GFortra We recommend that you install the most recent stable version for your platform You will download a gzipped tar file that you will have to unpack Once you have unpacked the file follow the instructions in the included PDF file to install the compiler 4 2 Using your unlisted compiler If you are using a compiler that is not already listed in the Makefile conf file you will have to make a new entry in that file You can test that the tool can find your compiler by typing make status One the tool can locate your compiler you may still have to edit the source code or Makefiles of the individual models in order to get the compiler flags to work correctly or to over
4. For the results presented here the field line shape is approximately parabolic over the region of the coma where the calculation occurs In principle the model can be used for any field line which threads the coma however below we present results from a representative field line which crosses the Sun comet line at 50km upstream of the nucleus e Gan L and Cravens T E 1990 J Geophys Res 95 6285 7 4 DSMC Please see the following papers for details about the DSMC model e Rubin M V M Tenishev M R Combi K C Hansen T I Gombosi K Altwegg and H Balsiger 2011 Monte Carlo modeling of neutral gas and dust in the coma of comet 1P Halley Icarus in press doi 10 1016 j icarus 2011 04 006 Tenishev V M M R Combi and M Rubin 2011 Numerical simulation of dust in a cometary coma Application to Comet Churyumov Gerasimenko Astrophys J 732 104 17pp doi 10 1088 0004 637X 732 2 104 Tenishev V M M R Combi and B J R Davidsson 2008 A global kinetic model for cometary comae The evolution of the coma of the Rosetta target comet Churyumov Gerasimenko throughout the mission Astrophys J 685 659 677 j ligj ulg e Combi M R W M Harris and W H Smyth 2004 Gas dynamics and kinetics in the cometary coma Theory and observations In Comets II M C Festou H U Keller H A Weaver eds U Arizona Press Tucson p 523 552 Combi M R 1996 Time dependent gas kinetics in tenuous planetary atmosp
5. H20 Driven V1 4 2n e Q 0 au 02 0 au 03 0 au 04 0 au 05 0 au 06 0 au 07 0_au_08 0 au 09 0 au 10 0 au 11 0 au 12 3 au 00 Q Q Q Q Qa Q Q Q Q WwW OD Q CHAPTER 2 INSTALLING AND RUNNING ICES MHD Hybrid DSMC H20 Driven V1 4 DSMC C0 C02 Driven V1 4 DSMC CO CO2 Driven V1 4 H20 Driven Jet V1 4 DSMC CO CO2 Driven Jet V1 4 DSMC H20 Driven V1 5 DSMC CO driven V1 5 DSMC CG 3 0 au 07 with Q 20 DSMC 3 0 au 07 with Q 20 DSMC CG 3 0 07 with Q 50 DSMC CG 3 0 au 07 with Q 50 DSMC Original ISSI Case V1 4 In addition you can find out the different cases available for the DSMC model by typing ICES 1 ds This command looks in the Data Coma directory and for each installed case looks in its DSMC directory and lists all the different particles which are simulated by the model Moreover it gives a short description of the case including its dimension and the version number of the files so that the users can check to make sure that they have the most up to date data files Typical output might look like Current cases available for CG 1 3 au 00 0 2 0 au 00 CG 2 7 au 00 CG 2 7 au 01 CG 2 7 02 CG 2 7 au 03 CG 2 7 au 04 CG 2 7 au 05 CG 2 7 au 06 CG 3 0 au 01 CG 3 0 au 02 CG 3 0 au 03 CG 3 0 au 04 CG 3 0 au
6. data from data files provided with the tool Currently the following models are available Coma Models Abbrev Description Physics ICES c Inner Coma Environment Simulator User interface amp tool DSMC Direct Simulation Monte Carlo Dust and neutral gas ELEC Electron Field aligned electrons HYB Hybrid Plasma kinetic ions fluid electrons MHD Magnetohydrodynamics Plasma single fluid Nucleus Models Abbrev Description Physics ICES_n Inner Coma Environment Simulator User interface amp tool K3D Nucleus Evolution Model Coma Sources Surface and Subsurface 1 1 Acknowledgments The ICES tool is the result of the work of several different research groups who have developed state of the art numerical models of different parts of the cometary environment On behalf of the ICES effort we have coordinated the use of these models to address the cometary environment in a self consistent and coupled manner and have produced a tool which provides the community easy access to model results The physics models were developed by the following research groups 5 CHAPTER 1 INTRODUCTION Abbrev Institution Location Responsible Persons ICES University of Michigan Ann Arbor MI K C Hansen DSMC University of Michigan Ann Arbor MI Michael Combi Valeriy Tenishev ELEC University of Kansas Lawrence Kansas Tom Cravens Ina Robertson HYB Institute for Theoretical Physics Braunschweig Germany Uwe Motschmann Technical University of Braunschweig
7. for internal sublimation we do not compute the gas flow rate but rather assume rapid transfer to the surface which is acceptable for shallow depths large porosities and steady state conditions We also consider dust drag representing the dust grain size distribution by 5 discrete categories differing in grain size For each azimuth depth and time we compute the critical grain size above which grains can be dragged by gas and leave the nucleus Those left behind form eventually an ice depleted permanent dust mantle The rate of growth of this mantle decreases considerably with repeated or bital revolutions therefore the results obtained here at the end of 5 orbits may be taken as representative The thickness of this mantle varies significantly over the nucleus surface Depending on latitude and on thermal conductivity but discarding as unphysical very high conductivities the dust mantle may be as thin as 1 cm and as thick as 10 cm This range is significant because the former is smaller than the diurnal skin depth while the latter exceeds it This means that on the nucleus surface there will be areas that show diurnal variation of activity rapid response to insolation but also areas of more constant activity The depth of unaltered material marked here by the crystallization front ranges between 1 m and several meters The size distribution of dust grains changes along the orbit be ing steeper at large distances In all cases it is ste
8. 07 7 3 Electrons The electron component of the cometary plasma is not a simple Maxwellian due to the several electron sources including the shocked and unshocked solar wind secondary electrons produced by the impact of solar wind electrons and photoelectrons In each case collisions with the neutral gas of the cometary coma modifies the electrons as they travel along magnetic field lines We model the electron population using methods described by Gan et al 1990 Gan constructed a model of the spatial and energy distributions of electrons in the vicinity of comet Halley The method involves the calculation of suprathermal electron fluxes using a two stream transport technique which included electron impact cross sections for rotational vibrational and electronic excitation of water molecules Their model 7 4 DSMC A1 also calculated electron temperatures for the thermal electron population and found that cold ionospheric electrons should indeed be present for cometocentric distances less than a few thousand km The Rosetta target comet 67 Churyumov Gerasimenko even near perihelion is a considerably weaker comet than Halley was in 1986 Nonetheless we have undertaken electron modeling for this comet near perihelion using the methods described in Gan et al 1990 In our model the electron transport is constrained by the magnetic field topology which we have extracted from the perihelion results of the MHD model discussed above
9. 14 The main work has been carried out by KC Hansen and Martin Rubin K3D Contact ICES tool can be download from Details of the current distribution documentation and other resources can be found at this location For questions regarding the ICES tool or any of the physics modules please contact lices adminQumich edul 1 3 SYSTEM REQUIREMENTS 7 Additional information about the ISSI comet modeling team the individual teams and the Rosetta mission can be found under the following links http www issibern ch International Space Science Institute ISSI Bern Switzerland ISSI comet home Electron model University of Kansas http www tu braunschweig de theophys research plasma Hybrid model University of Braunschweig MHD model University of Michigan http www esa int export SPECIALS Rosetta index html ESA Rosetta page http rosetta jpl nasa gov 1 3 System Requirements In order to install and run ICES the following minimum system requirements apply e ICES runs only under UNIX Linux operating systems This now includes Macintosh system 10 x because it is based on BSD UNIX ICES does not run under any Microsoft Windows operating system e A FORTRAN compiler must be installed to extract data from the MHD and Electron models e A C compiler is needed to extract data from the DSMC and the Hybrid simulations e Python must be instaled to extract data from the K3D model e The Perl Interpret
10. 27 5 x 1074 1 x 1027 6 x 1024 4 x 1074 7 5 x 1074 2 5 x 1074 5 x 1074 5 x 10 4 2 x 1022 3 x 1075 4 8 x 1022 5 x 1075 5 x 10 7 1 67 1022 The rest of the total production rate comes from others parent species 1 39 1027 5 1024 5 1024 1 1027 1 1027 5 1024 1 47 1027 6 1022 3 1025 0 5 1027 1 67 1022 85 5096 of productions as in the non jet case and the other 5096 of productions are due to the jet in an area centered on the sub solar point which represents 1096 of the total surface of the nucleus The size of the jet is adjusted so that the right dust size is lifted off that is to say 1 cm particles Location amp Status Solar Wind Case Rosetta Status R AU n cm v km s va km s B nT Angle E mV m a Instruments on 3 25 0 9 400 36 8 1 6 73 0 61 b 3 0 1 13 400 36 9 1 9 71 0 67 Lander Down 2 7 1 4 400 36 9 2 0 70 0 75 d 2 0 2 5 400 38 7 2 8 63 1 00 e Perihelion 1 3 6 0 400 43 7 4 9 52 1 54 CHAPTER 5 AVAILABLE CASES FOR THE COMA Location amp Status Neutral Coma Rosetta Status R AU Case Q 8 1 km Instruments on 3 25 Original ISSI 1x107 11x10 3 0 H20 driven 10 8 9 x 106 3 0 CO CO driven 2 1x 1027 8 9 x 106 Lander Down 2 7 Original ISSI and H20 driven 8x 1022 7 3 x 106 Lander Down 2 7 driven 2 2 x 10 7 7 3 10 2 0 Original ISSI 8x10 40 106 Perihelion 1 3 Original ISSI 5 1027 HE Chapter 6 Available Cases for the Nucle
11. 3 0 au 07 with Knudsen layer CG 3 0 au 07 with Knudsen laye Min Case Max Case Rendezvous Original Nominal Case CO CO2 Drive H20 Driven Low produ 67P CHURYUMOV GERASIMENKO CG 1 3 au 00 CG_1 3_au_01 CG_1 3_au_02 CG_2 0_au_00 CG_2 0_au_01 CG_2 0_au_02 CG_2 0_au_03 CG_2 7_au_00 CG_2 7_au_01 CG_2 7_au_02 CG_2 7_au_03 CG_2 7_au_04 CG_2 7_au_05 CG_2 7_au_06 CG_3 0_au_01 CG_3 0_au_02 CG_3 0_au_03 CG_3 0_au_04 CG 3 0 au 05 CG 3 0 au 06 CG 3 0 au 07 CG 3 0 au 08 CG 3 0 au 09 CG_3 0_au_10 CG 3 0 au 11 CG_3 0_au_12 CG_3 0_au_13 CG 3 0 au 14 CG_3 0_au_15 CG_3 0_au_16 CG_3 3_au_00 CG 3 5 au 01 CG_3 5_au_02 CG_3 5_au_03 4 14 x 1027 1 13 x 1078 8 x 1076 8 7 x 1026 4 14 x 10 6 2 4 x 1027 8 x 1025 2 4 x 1026 2 4 x 1026 2 2 x 1027 2 2 x 1027 2 4 x 1026 2 98 x 1027 6 x 1025 6 x 1025 2 1 x 1027 2 1 x 1027 6 1025 2 98 1027 5 5 1025 11 1027 6 6 1025 4 4 x 1025 8 25 x 1025 2 75 x 10 5 5 x 10 5 5 5 x 1025 2 08 x 1024 3 6 x 1026 1 x 1024 6 x 1026 1 05 x 1028 2 x 1028 Production Rate 7 62 1026 7 62 x 1076 4 x 1076 2 1027 7 62 x 1025 2 x 1076 2 x 1026 2 x 1026 2 x 1076 2 x 1026 2 x 1076 5 x 1025 5 x 1025 5 x 1025 5 x 1025 5 x 1025 5 x 1025 5 x 1025 1 x 1026 6 x 1025 4 x 1025 7 5 1025 2 5 x 1025 5 x 1025 5 x 1025 2 x 1074 3 x 1026 9 52 x 1023 5 x 1026 5 x 1026 1 67 x 10 1 39 1027 5 1074 5 x 1074 1 x 1027 1 x 1027 5 x 1024 1 47 10
12. DSMC will produce a hydrodynamic like solution in the collisional fluid limit We have developed a gas kinetic dusty gas DSMC comet model code It is capable of being run for 1D spherical 2D axisymmetric and fully 3D problems The photochemistry and photochemical kinetics for 42 CHAPTER 7 PHYSIC MODULE DETAILS the following parent molecules are now available H20 CO2 CO CH3OH H2CO C2H6 C2H4 C2H2 HCN NH3 and CH4 The model subsequently tracks the following dissociation products H H2 O OH C CH CH2 CH3 N NH NH2 C2 C2H C2H5 CN and HCO Refractory dust particles are included also as many simulation particles where the particle density and size distribution can be specified The fundamental descriptions and various applications of our DSMC comet model are found the papers listed above 7 5 K3D Please see the following papers for details about the K3D nucleus model e Rosenberg E D and D Prialnik 2009 Fully 3 dimensional calculations of dust mantle formation for a model of Comet 67P Churyumov Gerasimenko Icarus 201 740 749 doi 10 1016 j icarus 2009 01 028 K3D is a fully 3 dimensional model used to study dust mantle formation The model is essentially a thermal model taking into account conduction absorption of solar radiation emission of thermal radiation as well as heat released in crystallization of amorphous ice and absorbed in sublimation of crystalline ice While we consider a porous structure and allow
13. ICES User Manual Code Version 2 0 Kenneth Hansen Martin Rubin Nicolas Fougere November 11 2011 Contents 5 LITT 5 dud oA IRAE Rowe gus vinee ae ee rud I RS SE T RS 6 EEE ENDER S 7 a a Terre eee err a 7 9 21 Installins the code aa s 224 4 dog at SUM ee eee d a diea ko aa a 9 CUu 10 11 bb Seed eee eee es hed DENG 12 be eee ee ew ee NENNE 13 7 11 10 14 14 2 6 Testing the ICES_c pl coma codd llle 14 2 6 2 Testing the ICES n pl nucleus 15 i 15 The I ES c ol Oed i grae Bt eie PA SENGS 15 2 gt oma Exampled e se pa siche ede ed r sk eda eS 17 2 7 The ICES 1 18 oe ek eth oe NN 19 21 ICES c pl and Coma 21 11 oordinat diss I e e S he GS Goth ae ET ME ON REE ee Oe m EE Ge 21 12 Input trajectory 21 PET 22 3 2 ICES_n pl and Nucleus Modeld 25 qe 25 3 22 Input trajectory filg 2l 25 now sew rud IM RA a ee ee ee es SS 26 29 41 Installing compilers s sa 2 4 e k boxe BEN kjele Sate Ge wae REX wem Wo
14. ICES_v lt version_number gt tgz tar xf lt path_to_file gt ICES_v lt version_number gt tar The main directory ICES and its content as described above will be generated Installation of data files is described in the next section You should now be able to find additional information about the ICES utilities by typing 9 10 CHAPTER 2 INSTALLING AND RUNNING ICES make help ICES_c pl h ICES_n pl h 2 2 Installing coma data files Data files are distributed separately from the code because they are quite large in size You can find a list of all available cases for which data file exist at http ices engin umich edu ICES Download php as well as in Chapter 6 Note that coma and nucleus data directory structures are quite different due to the differences in the way the models function In order to install the data files begin by downloading a gzipped tar file of a case you are interested in from the above URL For the sake of discussion in this manual we will assume that you downloaded the 67P CG case which corresponds to the test case described below in Section 2 6 CG 1 3 au 00 tgz Once you have a file move to the Data Coma directory cd Data Coma and unpack the gzipped tar file tar xzf lt path to file gt CG 1 3 au 00 tgz This will make a new directory in the Data Coma directory that will contain all the necessary data files to extract information from each of the physics models If your tar program does not know abou
15. Nikolaos Gortsas MHD University of Michigan Ann Arbor MI K C Hansen Martin Rubin Tamas Gombosi The majority of work done to develop the ICES tool was supported by the following funding agencies institutions and individuals 1 2 The ISSI comet modeling team The ISSI comet modeling team was organized and is directed by Tamas Gombosi University of Michi gan Team meetings have been held at the International Space Science Institute ISSI in Bern Switzerland with funding provided by ISSI ICES The ICES tool the user interface and documentation and the coordination of tool issues was carried out by the Center for Space Environment Modeling CSEM of the University of Michigan under the funding from JPL as part of US Rosetta project The main development work has been carried out by KC Hansen and Martin Rubin DSMC Electrons Hybrid The comet Hybrid model was developed at the Institute of Theoretical Physics of the Technical University of Braunschweig under project MO539 10 of the Deutsche Forschungsgemeinschaft DFG Enhancements of the Hybrid model are supported by the Institute of Planetary Research of the German Aerospace Center DLR MHD The comet MHD model is part of the Space Weather Modeling Framework SWMF which was developed at the Center for Space Environment Modeling CSEM of the University of Michigan under the NASA Earth Science Technology Office ESTO Computational Technologies CT Project NASA CAN NCC5 6
16. Note that the MHD and hybrid models use a spherically symmetric source while the DSMC mode uses an axisymmetric source terms with day night asymmetry More detail about the parameters used to run each of the models can be found in the following papers 33 34 Case Heliocentric Dust Nucleus MHD Mean Le pm oam 7 EE 1 3 au at xo eno ES 500 CG 1 3 au 01 CG_1 3_au_02 CG_2 0_au_00 CG 2 0 au 01 CG_2 0_au_02 CG_2 0_au_03 CG_2 7_au_00 CG 2 7 au 01 CG 2 7 au 02 CG_2 7_au_03 CG_2 7_au_04 CG_2 7_au_05 CG_2 7_au_06 CG 3 0 au 01 CG_3 0_au_02 CG_3 0_au_03 CG_3 0_au_04 CG_3 0_au_05 CG_3 0_au_06 CG_3 0_au_07 CG_3 0_au_08 CG_3 0_au_09 CG_3 0_au_10 CG 3 0 au 11 CG_3 0_au_12 CG_3 0_au_13 CG 3 0 au 14 CG_3 0_au_15 CG_3 0_au_16 CG_3 3_au_00 CG 3 5 au 01 CG_3 5_au_02 5 to 150 CG_3 5_au_03 5 to 150 Knee distribution 3 for dust particles with radius up to 1mm and 4 beyond 40 to 300 40 to 300 25 to 250 5 to 150 5 to 150 CHAPTER 5 AVAILABLE CASES FOR THE COMA Additional Description Perihelion Original I min perihelion C max perihelion C Original ISSI C Detailed Chemis Min Case Max Case Original ISSI C H20 Driven H20 Driven CO CO2 Drive CO CO2 Drive H20 Driven K CO CO2 Driven H20 Driven H20 Driven CO CO2 Drive CO CO2 Drive H20 Driven K CO CO2 Driven H20 Driven CO Driven CG_3 0_au_07 with G CG 3 0 au 07 with CG_3 0_au_07 with G CG 3 0 au 07 with CG
17. are Variable Physical Quantity Status Indicates the validity of this data point outlined above X y Z Position Vx Vy Vz Neutral gas velocity components T Neutral gas thermal temperature N Neutral gas number density The DSMC dust output file contains the following variables Variable Physical Quantity Status Indicates the validity of this data point outlined above X y Z Position Vx R a Vy R a Vz R a Dust particles of radius a velocity components NUMBERDENSITY R a Dust particles of radius a number density MASSDENSITY R a Dust particles of radius a mass density 3 2 ICES N PL AND NUCLEUS MODELS 25 3 2 ICES_n pl and Nucleus Models 3 2 1 Coordinate system The coordinate system used is the nucleus models in ICES is a sun fixed coordinate system All angles are measured from the Sun Comet line the sub solar point e Latitude in degrees e Solar Hour angle SHA in degrees This is an angle similar to longitude except sun fixed 0 degrees corresponds to the sub solar point noon while 180 degrees corresponds to midnight 90 and 180 degrees correspond to west and east left and right when looking from the sun to the comet e Depth in meters The surface is given by using 0 Other positive numbers indicate the depth below the surface 3 2 2 Input trajectory file Input trajectory files should contain a list of points at which the user wishes to extract data from the models The may wish to use a l
18. as it should The test looks for the compilers set in Makefile conf compiles the code runs the ICES c pl tool using a sample trajectory file Tests traj_xaxis_example dat for all the models for the CG_1 3_au case and then compares the output with output files shipped with the distribution The test can be run by simply typing make test Assuming that you have the compilers set right and that the test works as it should the output should look like DSMC 1 3 00 CO0 dat identical within tolerance 0 001 zeros 1e 05 DSMC 1 3 au 00 Dust dat identical within tolerance 0 001 zeros 16 05 DSMC CG 1 3 au 00 H20 dat identical within tolerance 0 001 zeros 1e 05 Electron CG 1 3 au 00 dat identical within tolerance 0 001 zeros 1e 05 Hybrid CG 1 3 au 00 dat identical within tolerance 0 001 zeros 1e 05 MHD 1 3 au 00 dat identical within tolerance 0 001 zeros 1e 05 This indicates that the values in the files created by the test are identical to the files provided in the distribution to within 196 0 001 If there are larger differences in the files various error messages will appear Identical tests indicate that your code is compiled and working properly Note that the test compares to files that are located in the Tests directory If the tests are not identical the script will produce an error message to let the user know what the difference between the two files is The script will warn about the fi
19. ble and the documentation type make clean To remove the some additional files related to installation and any executable files that exist you can type make distclean Once you have make a clean or a distclean the code be recompiled as outlined above 20 CHAPTER 2 INSTALLING AND RUNNING ICES Chapter 3 Input and Output Files All input and output in the ICES tool should be in SI units with few exceptions Quantity Unit position m density H m3 velocity m s magnetic field Tesla pressure Pa Pascal temperature K Kelvin energy eV 3 1 ICES_c pl Coma Models 3 1 1 Coordinate system The coordinate system used in each of the models is defined as follows e X Points from the comet to the sun e Y Perpendicular to the X axis lying essentially in the Solar Ecliptic plane The vector then points in a sense that is retrograde to planetary motion More importantly this plane is the one which the models define as containing the solar wind magnetic field when a simple Parker Spiral field is used e Z Perpendicular to the X and Y axes and positive in a direction toward ecliptic north 3 1 2 Input trajectory file Input trajectory files should contain a list of points at which the user wishes to extract data from the models In general we might typically think of this file containing a list of points along a spacecraft trajectory However this is not a requirement It is possible for example to ask for a three di
20. case contains a VERSION file which give a version number so that the user can make sure they have the most up to date data files Moreover a SHORT_DESCRIPTION file provides a brief description of each case For more information about the individual models e g the size of the simulated domain see Chapter 7 12 CHAPTER 2 INSTALLING AND RUNNING ICES 2 4 Changing the default settings As outlined in the system requirements Section L 3 the ICES code can be run only under UNIX Linux this includes Mac version 10 x Because the tools is provided as source code it must be compiled before it can be used Before compiling the source code you must make sure that you have a Fortran 77 and 90 95 compiler as well as a C compiler installed on your system The codes in the ICES distribution have been tested on the following systems with the listed compilers Compiler Abbrev Source code type Operating System Name Provider DSMC C Mac Os X g GNU SGI Altix g GNU ELEC Fortran 77 Mac OS X gfortran GNU f95 NAG SGI Altix ifort Intel HYB C Mac OS X g GNU SGI Altix g GNU MHD Fortran 77 Mac OS X gfortran GNU f95 NAG SGI Altix ifort Intel K3D Python Mac OS X python If your compiler does not appear it may still work To find out how read this section as well as the sections in the next chapter on installing compilers Sections A I and 2 In order to compile the code you must edit the Makefile conf fi
21. ce the small non zero value is likely machine dependent the numbers in the two files may be very different often more than an order of magnitude However compared to the value of uz they are orders of magnitude smaller and the errors are physically insignificant When errors like this occur they can be ignored e If the values with errors do not seem to be near zero and are therefore physically significant a large error probably indicates that you have a problem with the installation and or the compiler You may need to contact the ICES administrators 32 CHAPTER 4 TROUBLESHOOTING Chapter 5 Available Cases for the Coma The ICES was develop as part of an ISSI comet modeling project that concentrated on the Rosetta mission target comet 67P Churyumov Gerasimenko The first cases that are available for use with the tool therefore are for comet 67P CG Other comets and cases will be added periodically 5 1 67P Churyumov Gerasimenko Comet 67P CG has been observed on a number previous perihelion passages but not intensively Once it was identified as the Rosetta target well after the most recent perihelion passage a more concerted effort was begun to monitor at least its outgoing leg The ISSI comet modeling team chose to model the comet at four representative heliocentric radial distances that represent either significant times of the mission or serve to span the range of plasma environments that can be expected during the mission T
22. come any compiler specific bugs that may still be in the code or in the compiler itself From experience we know that since we have ported this code to several different machines and compilers that for most platforms using a new compiler should be fairly simple however there may still be some issues For each model we list below the locations of Makefile which you may need to modify e DSMC DSMC makefile e Electron Electron Makefile e MHD MHD src Makefile e Hybrid Hybrid Makefile For additional problems you may have to contact us to see if we are able to help you with you individual problem 29 30 CHAPTER 4 TROUBLESHOOTING 4 8 FAQ 4 3 1 MHD Unable to read from opened MHD file The MHD data files are binary and they are machine specific Apple Macintosh computers with Power PC PPC G5 processor or before use a special format All other machines including Apple computers with Intel processors use the more common format The following error read iblock file unable to read from opened MHD file named MHDRestart blk00001 rst generally indicates that you have downloaded the incorrect data files for your computer s processor You can check the type of your machine s processor by typing the following command uname p If the result is powerpc then you should use the version of the files on the ICES web page labeled Version for MACs with PPC Processors G5 or before Otherwise you download the files with the label Ve
23. ction In order to install the data files begin by downloading a gzipped tar file of a case you are interested in from the above URL For the sake of discussion in this manual we will assume that you downloaded the 67P CG case which corresponds to the test case described below in Section 2 6 K3D_CG_01 tgz Once you have a file move to the Data Nucleus directory cd Data Nucleus and unpack the gzipped tar file tar xzf lt path_to_file gt K3D_CG_01 tgz This will make a new K3D directory in the Data Nucleus if it does not exist year and will add to it the CG 01 directory that will contain all the necessary data files to extract information for this case If your tar program does not know about the z flag you will have to install the data files in two steps gunzip lt path_to_file gt K3D_CG_01 tgz tar xf lt path_to_file gt K3D_CG_01 tar Other data files can be download from the web site and installed in a similar manner The data is ordered by case first and then by the orbit inbound or outbound and finally by the heliocentric distance After installation of the case K3D CG 01 the Data Nucleus K3D folder should look like the following Data Nucleus K3D CG_01 OG 01 cgf CG 01 011 5 7au dat CG 01 02i 1 3au dat CG 01 01i 1 4au dat CG 01 011 1 5au dat DETAILS SHORT DESCRIPTION VERSION Each case contains a DETAILS file which provides some details about the simulation and physical parameters for that case In addition each
24. directory for available cases and lists them as well as which models are available for this case Also indicated is the version number of the files so that the users can check to make sure that they have the most up to date data files Typical output might look like Current nucleus models available K3D Model Case Version Description K3D CG 01 1 0 Nominal K3D model In addition you can find out the different orbits and heliocentric distances available for each case by typing ICES n pl sv Note that this command will produce a very lengthy output Typical output might look like Current nucleus models available K3D Model Case Orbit Heliocentric distances K3D CG 01 011 5 7 021 1 3 1 4 1 5 1 6 1 7 1 8 1 9 5 4 5 5 5 6 5 7 ap ph 020 1 3 1 4 1 5 1 6 1 7 1 8 1 9 5 4 5 5 5 6 5 7 ap 03i 1 3 1 4 1 5 1 6 1 7 1 8 1 9 5 4 5 5 5 6 5 7 ap ph 03o 1 3 1 4 1 5 1 6 1 7 1 8 1 9 5 4 5 5 5 6 5 7 ap 04i 1 3 1 4 1 5 1 6 1 7 1 8 1 9 5 4 5 5 5 6 5 7 ap ph 040 1 3 1 4 1 5 1 6 1 7 1 8 1 9 5 4 5 5 5 6 5 7 ap Obi 1 3 1 4 1 5 1 6 1 7 1 8 1 9 5 4 5 5 5 6 5 7 ap ph 050 1 3 1 4 1 5 1 6 1 7 1 8 1 9 5 4 5 5 5 6 5 7 ap To extract data for modules you use ICES n pl with 6 arguments in the command line The command we use to carry out the test make test is ICES n pl model K3D Tests nucleus input example dat 00 01 031 2 5 test temp The arguments to the scripts in required order are as follows 1 The model we wish to use model K3D 2 A trajectory f
25. ed as a tar gzip file of the source code This code must be compiled before it can be used The tool also makes use of data files which are installed separately from the tool because the data files are very large in size Basics for using the tool are found in this chapter The next chapter addresses problems that may arise or more complex ways of interacting with the tool The top level directory of the ICES tool contains the following subdirectories and files Data Directory containing the data files needed by each model Doc Documentation ICES_c pl Main script runs data extraction for COMA models ICES_n pl Main script runs data extraction for NUCLEUS models Makefile Utility for compiling source codes Makefile conf Configuration file for Fortran and C compilers Models Directory containing source code for all models README Short description of how to install and run the code Scripts Useful scripts Tests Contains sample files and files for comparison tests 2 1 Installing the code The first step in installing the code is untarring the distribution Change directories to the location at which you would like the ICES tool to reside cd path to desired installation location Next untar the code tar xzf path to file gt ICES v lt version number gt tgz This will unpack in a new directory ICES If the tar program does not know about the z flag you will have to open the distribution in two steps gunzip lt path_to_file gt
26. eper than that assumed for the nucleus
27. er must be installed e A minimum of 1GB of RAM is needed to run the ICES tool Roughly 50 MB of hard disk space is needed to install the ICES tool not including the simulation data files e Each simulation case requires an additional 1 GB of hard disk space e n order to generate the documentation you must have LaTeX installed The PDF generation requires the dvips and ps2pdf utilities To generate the HTML version you also must install the latex2html package Please note that C Perl and Python general come automatically installed on many UXIX Linux systems 1 4 Documentation The ICES tool is delivered with both a PDF version and an HTML version of the documentation The PDF version is located at Doc ICES_manual pdf and can be open with Adobe Reader or a similar product The HTML version can be accessed by opening the file Doc HTML index html in your favorite web browser You can also access the user manual online by pointing your browser to http ices engin umich edu ICES It is also possible to access the source LaTex files for the documentation and to build new version of the PDf and HTML versions The LaTex source is found in Doc Tex and the new version can be built by typing 8 CHAPTER 1 INTRODUCTION make PDF make HTML in the main directory of the distribution Output files from these two commands are located in the Doc Tex directory Chapter 2 Installing and Running ICES The ICES tools are deliver
28. heres The cometary coma Icarus 123 207 226 Kinetic approaches to modeling the cometary coma recognize that in much of the coma collisions occur between molecules but not enough to maintain thermal equilibrium in large and sometimes critical regions Fully kinetic models based on the Direct Simulation Monte Carlo DSMC method have been applied to the cometary coma as a practical method to solving the general collisional Boltzmann equation DSMC was developed to simulate the transition regime where the mean free path of molecules is too large for continuum hydrodynamics to be applicable Therefore gas molecules are modeled as a sample of individual particles and simulated as they move around within a grid colliding with other particles and with solid objects if any Macroscopic properties such as density velocity and temperature are computed by performing the standard kinetic theory averaging of particle masses locations velocities and internal energies over the particle distribution function DSMC is based on the rarefied gas assumption that over a short time interval or step the molecular motion and the intermolecular collisions are uncoupled and therefore can be calculated independently Molecules are moved over the distances appropriate for this time step followed by the calculation of a representative set of collisions The time step is small compared to the mean collision time and the results are independent of its actual value
29. hese locations and their relation to the mission milestones have changed during the time that these simulations were developed but the cases are still representative of the range of environments that the comet will experience In order to model the comet for the cases listed above we must choose representative solar wind con ditions So that the models will be reasonably self consistent we have based the solar wind conditions on nominal values at 1AU At that location we use u 400 km s n 10cm Te 1x 10 K T 5x 10 and B 7nT confined to the ecliptic plane making an angle representative of the Parker spiral at LAU We then use an extrapolation to obtain the conditions for each of the cases The above Table also gives values in the upstream solar wind for density n velocity v magnetic field magnitude B and Parker spiral angle the Alfv n speed va and the electric field E Clearly these values are only representative of the conditions that comet 67P CG may encounter during the Rosetta mission however as average values they will give a good idea of the type and scale of the expected interaction between the comet and the solar wind Below an additional table indicates the values of the cometary neutral production rate which are applied in the models Both the gas production rate and the ionization scale length depend on heliocentric distance The table indicates the values for these parameters that we have adopted
30. highlighted by the code In order to investigate if your installation is working properly and if these errors are significant or not we provide some hints for things to look for e Open the two files containing the results of the corresponding code The baseline file the good file which is shipped with the ICES distribution can be found in the following ICES subfolder Tests Test_CG_1 3_au_00 and the corresponding output file created on your machine during the make test procedure in test temp 4 8 FAQ 31 For example the files of the MHD code can be found at Tests Test 00 1 3 00 MHD CG 1 3 au 00 dat test temp MHD CG 1 3 au 00 dat e You will need to look at the two files in detail starting with the specific line and variable called out by the script Since the code only locates the first error there may be more possibly larger differences that you should also examine Graphical differencing tools are great for this exercise tkdiff xdiff Another simple examination method is to import both files into a spreadsheet e You want to determine if the differences you find are significant or not Often differences are not significant because they represent fluctuations around zero In the MHD simulation for instance the upstream boundary conditions for the solar wind velocity are u 400 km s u 0 u 0 Far upstream however due to roundoff errors and UZsw are very small but not exactly zero Sin
31. hout some editing of the source code See the later sections on installing compilers Sections I T and 2 in order understand how you can make the codes work with your compiler If you do not have a Fortran or C compiler you may try to install the free GNU f95 and g compilers See the later sections on installing compilers 2 5 Compilation Before you can use the ICES c pl or ICES n pl tools to extract data from the simulation results you must compile the extraction codes for each physics model you are interested in In order to compile all models type the following commands into the terminal make ALL 14 CHAPTER 2 INSTALLING AND RUNNING ICES Or to install selected components only e g the Direct Simulation Monte Carlo and Hybrid models type make DSMC HYB The user can check the status of which models have been compiled and are ready to be used by typing make status In the case where all the models are installed the output should look like MHD Compiled Hybrid Compiled Electron Compiled DSMC Compiled K3D Not yet compiled F90 compiler found usr local bin f95 F77 compiler found usr local bin f95 C compiler found usr bin g Py compiler found usr bin python Note that the compilers are also looked for as discussed earlier in Section 2 4 2 6 Testing the code 2 6 1 Testing the ICES c pl coma code The ICES tool ships with a very simple way of testing to make sure that the code is working
32. iffusive processes through appropriate source terms Here we present a few details about the aspects of BATSRUS that are relevant to the solar wind comet interaction and refer the reader to an extensive literature related to the numerical algorithms used in the code A review of many of the fundamental aspects of the model algorithms and their application to comets can be found in papers listed above an references contained in them One of the most important features of BATSRUS is the ability to easily adapt the grid to resolve specific regions of space BATSRUS utilizes the approach of adaptive blocks Adaptive blocks partition space into regions each of which is a regular Cartesian grid of cells called a block If the region needs to be refined then the block is replaced by 8 child sub blocks each of which contains the same number of cells as the parent block The use of cells of varying sizes allows us to resolve features of vastly different length scales In the simulations presented in this paper we are able to resolve the body the diamagnetic cavity and the solar wind neutral cloud interaction even though these occur at vastly different length scales Note that the adaptive mesh allows us to use an extremely large simulation box and therefore self consistently model the mass loading and subsequent slowing of the plasma upstream of the bow shock In the model all processes associated with mass loading ionization charge exchange recombination e
33. ile Test nucleus_input_example dat 2 8 RECOMPILATION AND CLEAN UP 19 A case for which data is available CG_01 The orbit from which you want to extract data 031 The heliocentric distance you want to consider 2 5 Orr um e The directory where you want output to go test_temp The format for the trajectory file is addressed in the following chapter As outlined above the case argument should be the name of one of the directories in the Data Nucleus directory Note that the output directory must exist before the tool runs If it does not exist you will loose the output You can send the output to your current directory by using a command something like ICES n pl model K3D Tests nucleus input example dat CG_01 031 2 5 66 99 where here the indicates send output to the current directory Arguments can also be typed in lowercase An output file is created for the parameters you have selected Output files are named with the name of the model followed by the name of the data input file case From the above test command the following output file would be generated K3D__CG_01_03i_2 5au dat For information of the format of the extracted data see the next chapter 2 8 Recompilation and clean up Anytime you wish to change the compiler or are trying to recover from an error you probably should clean out any intermediate files that were created To clean up files o mod which were used to build the executa
34. ist of points at fixed LAT SHA and then scan across depth Or perhaps use depth 07 for all points and grid the surface However in general there is no restriction on the way the points are selected or ordered The trajectory files should have three columns in it corresponding to the three dimensional location of the desired points LAT SHA D Columns should be separated by spaces only Note that the locations should be given in meters For the downloadable version data should start after a line containing the text START Anything in the file before this command is ignored by the processing codes This conveniently allows the user to add notes or other information about the trajectory file in the header A sample trajectory file can be found in Tests nucleus_input_example dat MODEL CG1 Latitude deg Hour Angle deg Depth m START 90 0 0 0 1 0 80 0 20 0 0 0 70 0 40 0 0 01 60 0 60 0 0 02 50 0 80 0 0 0 40 0 100 0 0 06 30 0 120 0 0 07 20 0 140 0 0 08 10 0 160 0 0 09 0 0 180 0 0 1 10 0 200 0 0 5 20 0 220 0 1 0 30 0 240 0 2 0 40 0 260 0 5 0 50 0 280 0 10 0 60 0 300 0 20 0 70 0 60 0 50 0 80 0 40 0 70 0 90 0 20 0 99 9 The format of the numbers in the individual columns should not matter 26 CHAPTER 3 INPUT AND OUTPUT FILES For the GUI version the user does not have to type the text START Thus in order to use the same sample file which contains points along the x axis with the GUI version the use
35. le in order to set the default compilers for your system You must make a selection for the Fortran 90 95 F90 Fortran 77 F77 and the C compilers No selection is necessary for Python A sample entry from the Makefile conf file is below GNU Compiler Known to work on MAC OSX COMPILE 90 gfortran NAG Compiler Known to work on MAC OSX COMPILE 90 95 INTEL Compiler Known to work on SGI Altix HCOMPILE f90 ifort In this example the GNU gfortran compiler is selected for compiling F90 files The selected compiler should not have a in front of it All other compilers should be commented out using the symbol The F77 compiler should typically be set the same as the F90 compiler i es a ah E Ee ras LE E jern Del E Select a compiler for FORTRAN 77 codes In most cases should be set the same as for the FORTRAN 90 95 codes a si a en lp at eee ee ie a St SS es en dt Set the same as for FORTRAN 90 95 2 5 COMPILATION 13 COMPILE 77 COMPILE f90 Set different than for FORTRAN 90 95 GNU Compiler COMPILE 77 gfortran In this example the Makefile conf has the F77 compiler set equal to the F90 compiler If the COMPILE f77 gfortran then the F77 compiler could be set to something different tha
36. me of the particle for the DSMC model From the above test command the following output files would be generated DSMC_CG_1 3_au_00 CO dat DSMC CG 1 3 au 00 C02 dat DSMC 1 3 00 Dust dat DSMC CG 1 3 au 00 H20 dat Electron CG 1 3 au 00 dat Hybrid CG 1 3 au 00 dat MHD CG 1 3 au 00 dat 2 7 2 Coma Examples Here we give a few examples of ways to run the ICES c pl tool As outlined above the following command is the one we use in the make test command ICES_c pl Tests traj_xaxis_example dat CG 1 3 au 00 test temp ALL If you wish to use only the plasma models MHD and Hybrid you could use ICES_c pl Tests traj xaxis example dat CG 1 3 au 00 test temp MHD HYB If you wanted to place the output in the current working directory and only wanted to know what the neutral distribution was you could use only the DSMC by typing ICES_c pl Tests traj xaxis example dat CG 1 3 au 00 DSMC For information of the format of the extracted data see the next chapter 18 CHAPTER 2 INSTALLING AND RUNNING ICES 2 7 3 The 1 5 n pl script In script order to run the code to extract nucleus information use the Perl script ICES_n pl provided in the main directory As with all scripts provided in the ICES tool you can get help about running the script by typing ICES_n pl h Additionally you can find out which data files have been installed and which are ready to be used by typing ICES_n pl s This command looks in the Data Nucleus
37. mensional grid of regularly spaced points or any other list of points that might be desirable The trajectory files should have three columns in it corresponding to the three dimensional location of the desired points X Y Z Columns should be separated by spaces only Note that the locations should be given in meters For the downloadable version data should start after a line containing the text START Anything in the file before this command is ignored by the processing codes This conveniently allows the user to add notes or other information about the trajectory file in the header A sample trajectory file which represents points along the x axis of the models can be found in Tests traj_xaxis_example dat 21 22 CHAPTER 3 INPUT AND OUTPUT FILES This is a sample file which contains points along the x axis START 3 0e9 2 0e9 1 0e9 9 0e8 0 0 0 0 0 0 0 0 8 0e8 0 0 0 0 0 0 0 The format of the numbers in the individual columns should not matter For the GUI version the user does not have to type the text START Thus in order to use the same sample file which contains points along the x axis with the GUI version the user has to enter the trajectory as follow This file contains point which will be out of range for some of the physics models In this case the physics model detects this and returns files that flag the error See the next section 3 1 3 Output files Output files are
38. n the F90 compiler The C compiler is set similarly You can check to see if the tool can located the compilers that you have selected by typing make status This command lists the current state of compilation of the different physics models as well as the status of finding the different compilers A sample output from this command might be Running ICES v1 0b OS Darwin Kernel Version 8 11 1 Wed Oct 10 18 23 28 PDT 2007 root xnu 792 25 20 1 RELEASE 1386 MHD Not yet compiled Hybrid Not yet compiled Electron Not yet compiled DSMC Not yet compiled K3D Not yet compiled F90 compiler NOT FOUND ifort F77 compiler NOT FOUND ifort C compiler found usr bin g Py compiler found usr bin python One or more compilers were not found Edit Makefile conf First note that this command tells you the version of ICES that you are running as well as giving you information about the computer system that you are using Following this the results would indicate that you have not yet compiled any of the codes this is described in the next section In addition it indicates that the tool cannot find the ifort Intel compiler which you have selected to compile the Fortran codes It did however find the g compiler for the C codes If your compiler does not appear in the list of compliers in the Makefile conf file then you will have to add it Because the code has not been tested with your compiler the codes may not work wit
39. olerance in the FAQ section to learn where the corresponding files can be found 2 6 2 Testing the ICES n pl nucleus code This test has not yet been implemented It is coming 2 7 Running the code and examples 2 7 1 The ICES c pl script In order to run the code to extract coma information use the Perl script ICES c pl provided in the main directory As with all scripts provided in the ICES tool you can get help about running the script by typing ICES_c pl h Additionally you can find out which data files have been installed and which are ready to be used by typing ICES c pl s This command looks in the Data Coma directory for available cases and lists them as well as which models are available for this case Also indicated is the version number of the files so that the users can check to make sure that they have the most up to date data files Typical output might look like Current cases available in Data Coma OG 1 3 00 MHD Hybrid DSMC Electron Original ISSI Case V1 4 OG 2 0 00 MHD Hybrid DSMC Electron Original ISSI Case V1 4 CG 2 7 00 MHD Hybrid DSMC Original ISSI Case V1 4 CG 2 7 au 01 ed MHD DSMC H20 Driven V1 4 CG 2 7 au 02 zu DSMC H20 Driven V1 4 CG 2 7 au 03 MHD DSMC CO CO2 Driven V1 4 CG_2 7_au_04 DSMC C0 C02 Driven V1 4 CG 2 7 05 MHD DSMC H20 Driven Jet V1 4 CG 2 7 au 06 MHD DSMC CO CO2 Driven Jet V1 4 0 3 0 01 MHD
40. other data files What follows is two blocks of data for each point in the trajectory file The first block of data includes the upward flux of electrons while the next block contains the downward flux of electrons The format is as follows 9 000E 07 0 000E 00 0 000 400 X Y 2 Upward Flux 1 10 7 363E 04 8 687E 04 7 363E 04 5 409E 04 1 220E 05 1 899E 05 11 20 5 207E 05 5 439 05 5 956E 05 6 573E 05 6 766 05 7 287E 05 21 30 9 293E 05 9 478E 05 9 869E 05 1 044E 06 1 069E 06 1 123E 06 9 000E 07 0 000E 00 0 000 400 X Y 2 Downward Flux 1 10 7 363E 04 5 409E 04 3 889E 04 1 133E 05 1 129E 05 1 124E 05 11 20 1 098E 05 1 093E 05 1 088E 05 1 082E 05 1 077E 05 1 072E 05 21 30 1 044E 05 1 038E 05 1 033E 05 1 027E 05 1 021E 05 1 016E 05 where here the first block indicates that this contains the upward flux for the listed location X Y Z Each line of the block starts with the bin range of that row followed by the fluxes in each bin The second block lists the same X Y Z but now contains the downward flux DSMC Files for the DSMC model follow the format of the MHD and Hybrid models As with the Hybrid model the DSMC model is capable of computing distribution functions of the neutral molecules In addition the DSMC model can compute distribution functions of the dust particles However at this time we are only able to provide the moments of the distribution function Currently available quantities in the DSMC files for the neutrals
41. r has to enter the trajectory as follow 90 0 0 0 1 0 80 0 20 0 0 0 70 0 40 0 0 01 60 0 60 0 0 02 50 0 80 0 0 0 40 0 100 0 0 06 30 0 120 0 0 07 20 0 140 0 0 08 10 0 160 0 0 09 0 0 180 0 0 1 10 0 200 0 0 5 20 0 220 0 1 0 30 0 240 0 2 0 40 0 260 0 5 0 50 0 280 0 10 0 60 0 300 0 20 0 70 0 60 0 50 0 80 0 40 0 70 0 90 0 20 0 99 9 This file contains point which will be out of range for some of the physics models In this case the physics model detects this and returns files that flag the error See the next section 3 2 3 Output files Output files are written into the directory listed in the ICES_n pl command A unique output file is created for the output from each model selected Output files are named with the name of the model followed by the name of the data input file case used A typical output files might be CG 01 031 2 5au dat Most output files have similar formats In these files interpolated values follow the START line the file Above this line is header information which may be unique the model In each file there will be a list of variables There may be additional information in the header as well Each quantity is listed in a column K3D K3D output files contain the following variables 3 2 Column 00 10 C2 l2 NN ke RP EP RP RP RP RP 0 0066 01 40 ICES N PL AND NUCLEUS MODELS Physical Quantity Status Latitude Solar hour angle
42. ron temperatures but cannot determine either individually because we do not know the ratio T Te Hybrid The hybrid model can generated distribution functions of ions However in this version of ICES we are only able to make available moments of the distribution function Available quantities are Variable Physical Quantity X y Z Position Bx By Bz Magnetic field components Ex Ey Ez Electric field components rhosw Solar wind ion number density uswx uswy uswz Velocity components of the solar wind ions rhohi Oxygen ion number density uhix uhiy uhiz Velocity components of Oxygen ions Electron The data format of the Electron data files are quite a bit more complicated than the data products from the other models This is because the files contain the electron flux in a list of energy bins at each point There are 185 energy bins and in each we give both the upward and downward electron flux The file contains the 24 CHAPTER 3 INPUT AND OUTPUT FILES data at each point in blocks The first block in the files is a header which indicates the energy values in keV of each energy bin The first lines of this block look like Energy Bins 1 10 0 25 0 75 1 25 1 75 2 25 2 75 11 20 5 25 5 75 6 25 6 75 7 25 7 75 21 30 10 50 11 50 12 50 13 50 14 50 15 50 where the first entry is the bin number with ten bins per row In that row then follow the energy values for each bin The data begins with a START line as in the
43. rsion for most systems 4 3 2 The last line of the output file is missing Due to the implementation of the gcc compiler the input trajectory file must end with at least one carriage return to a blank line If this is not the case in your file the last line of the trajectory file will not be interpolated to and the line will be missing from the output file of some or all of the different models depending on the selected compilers You can easily fix this by adding one or more blank lines to the end of the trajectory file 4 3 3 Errors when running make test See the section on Testing the Code 4 3 4 Difference exceeds tolerance in make test There are various reasons why you might receive this error message Typically the reason is dependent on what machine and or compiler you are using Most commonly the error is a result of how floating point mathematics when doing interpolations on your trajectory file and the associated round off errors are handled These round off errors can lead to slightly different results on different machines As part of make test the output files in the distribution are compared with the output files created on your machine to check for differences The error message indicates the first point in a trajectory file where the percent difference between the two data files exceeds a given tolerance for ICES currently 0 1 96 Some times these errors are significant but often they are not even when
44. rst difference that it finds Possible errors include e Missing file file can be missing for several reasons including The Hybrid model files are not compatible with Mac computers running Power PC processors so they are missing On a PPC Mac there will be an error associate with this 2 7 RUNNING THE CODE AND EXAMPLES 15 The MHD model files require different formats on Mac computers running Power PC processors See the FAQ If the code fails for some other reason then file will be missing You will have to look back at the output for a reason for the failure or consult the FAQ e Different number of lines in the two files See the FAQ e Difference exceeds tolerance This error may mean that there is a real problem or it may just mean that because you are using a different machine with different compilers that the numbers are slightly different but nothing to worry about See the FAQ for a detailed description of how to tell the difference It is possible to compare the results of runs on various machines for the same case using the Scripts TestCompare pl script This script is responsible for the comparison done in the test outlined above Type Scripts TestCompare pl h to learn more about this script and it s uses You can for example change the tolerance which determines if the files are identical or not In case you want to further investigate the output of the make test read also Difference exceeds t
45. s law This model resolves physical structures down to a time scale below the inverse lower hybrid frequency The code solves the spatial part of the Maxwell equations on an arbitrary curvilinear hexahedral ordered grid by applying finite difference schemes The time integration is done by a cyclic leapfrog scheme with a modified current advancement method 3 In addition in order to achieve a higher resolution of dispersive effects the magnetic field time evolution is obtained from a subcycling leapfrog method 1 We conduct a series of hybrid plasma simulations for four different heliocentric distances covering the range between 3 25 AU and 1 30 AU which corresponds to important stages of the Rosetta mission The used physical parameters are described in 4 1 Bagdonat T and Motschmann U 3d hybrid simulation code using curvilinear coordinates J Comp Phys 183 p 470 485 2002 2 Bagdonat T and Motschmann U From a weak to a strong comet 3d global hybrid simulation studies Earth Moon and Planets 90 p 305 321 2002 3 Matthews A P Current advance method and cyclic leapfrog for 2D multispecies hybrid plasma simulations J Comp Phys 112 p 102 116 1994 4 Hansen K C Bagdonat T Motschmann U Alexander C Combi M R Cravens T E Gombosi T I Jia Y D and Robertson I P The Plasma Environment of Comet 67P Churyumov Gerasimenko Throughout the Rosetta Main Mission Space Science Reviews 128 p 133 166 20
46. s_example dat CG 1 3 au 00 test temp ALL The arguments to the scripts are as follows V1 0 V1 0 V1 0 V1 0 2 7 RUNNING THE CODE AND EXAMPLES 17 1 A trajectory file Test traj_xaxis_example dat 2 A case for which data is available CG 1 3 au 00 3 The directory where you want output to go test temp 4 Which module you want to extract data from 1 or more items can be listed The format for the trajectory file is addressed in the following chapter As outlined above the case argument should be the name of one of the directories in the Data Coma directory Note that the output directory must exist before the tool runs If it does not exist you will loose the output You can send the output to your current directory by using a command something like ICES_c pl Tests traj xaxis example dat CG 1 3 au 00 ALL 66 99 where here the indicates send output to the current directory The final argument is the list of modules that you wish to extract data from Available options include Argument Model DSMC Direct Simulation Monte Carlo model ELEC Electron model HYB Hybrid model MHD Magnetohydrodynamics model ALL Extract data from each of the above models Arguments can also be typed in lowercase An output file is created for the output from each model selected and for each particle run by the DSMC Output files are named with the name of the model followed by the name of the data input file case used and the na
47. t the z flag you will have to install the data files in two steps gunzip path to file gt CG 1 3 au 00 tgz tar xf path to file gt CG 1 3 au 00 tar Other data files can be download from the web site and installed in a similar manner The data is ordered by case first and then by the model After installation of the case CG_1 3_au_00 the Data Coma folder should look like the following Data Coma CG 1 3 au 00 DETAILS DSMC Electron HYB MHD SHORT DESCRIPTION VERSION Every sub folder in the case directory contains the data of the corresponding model Each case contains a DETAILS file which provides some details about the simulation and physical parameters for that case In addition each case contains a VERSION file which give a version number so that the user can make sure they have the most up to date data files Moreover a SHORT DESCRIPTION file provides a brief description of each case For more information about the individual models e g the size of the simulated domain see Chapter 7 2 3 INSTALLING NUCLEUS DATA FILES 11 2 3 Installing nucleus data files Data files are distributed separately from the code because they are quite large in size You can find a list of all available cases for which data file exist at http ices engin umich edu ICES Download php as well as in Chapter 6 Note that coma and nucleus data directory structures are quite different due to the differences in the way the models fun
48. tc are handled through appropriate sources terms These are implemented in the same manner as the 39 40 CHAPTER 7 PHYSIC MODULE DETAILS source terms used in our previous study of the comet Hale Bopp Differences from that paper only require adjusting the gas production rate to that of comet 67P CG and adjusting the photoionization scale length for heliocentric distance 7 2 Hybrid Nikolaos Gortsas Uwe Motschmann Ekkehard K uhrt Technical University of Braunschweig and German Aerospace Center DLR Contact nikolaos gortsas dlr de u motschmann tu bs de A fully three dimensional hybrid plasma simulation code developed since the year 2000 at the Technical University of Braunschweig 1 2 is applied to the study of the plasma environment of Comet 67P Churyomuv Gerasimenko the target comet of ESA s Rosetta Mission The hybrid model is characterized by a semi kinetic treatment of the particle dynamics In the presented calculations we consider two different species solar wind protons and the much heavier cometary ions The particle dynamics of each species is described by Newtonian equations of motions with the Lorentz force and a collision force modeling interactions with the neutral gas The electrons are assumed to be a massless charge neutralizing fluid which is described by conservation laws An equation for the electric field is derived from the electron model while the time evolution of the magnetic field is obtained from Faraday
49. ty of this data point outlined above 7 Position n Ion and electron mass density see discussion below Vx Vy Vz Velocity components Bx By Bz Magnetic field components p Thermal pressure in Pascals p nkT We need to note several unique aspects of the MHD files First because the MHD simulations are single species there is no way of knowing the ion composition Near the comet the plasma would have an average mass of 18 amu H20 and far upstream of the comet the average mass would be I amu In regions where ions are mixed it is not possible to determine the average mass For this reason the mass density for the comet is given in amu m Near the comet or in the far upstream solar wind the number density can be determined In mixing regions it cannot The second important aspect of the MHD output to note is that the pressure is provided rather than the temperature The two are obviously related P neKT Y n KT 3 1 where ne Te refer to the electron and ns refer to individual ion species From the above discussion it should be clear that it is not always possible to determine ne and ns Assuming that we are in a region where we know the average mass and also assuming that the temperature of all ion species is the same yields p P 6 1 3 2 where i indicates a sum over all the ions p is the mass density and lt m gt is the average mass In this region we can determine the sum of the ion and elect
50. us 38 CHAPTER 6 AVAILABLE CASES FOR THE NUCLEUS Chapter 7 Physic Module Details 7 1 MHD Please see the following papers for details about the MHD model e Hansen K C T Bagdonat U Motschmann C Alexander M R Combi T E Cravens T I Gom bosi Y D Jia and I P Robertson The plasma environment of Comet 67P Churyumov Gerasimenko throughout the Rosetta main mission 2007 Space Sci Rev 70 133 166 doi 10 1007 s11214 006 9142 6 e Gombosi T I K C Hansen D L De Zeeuw M R Combi and K G Powell 1997 MHD simula tion of comets The plasma environment of comet Hale Bopp Earth Moon and Planets 79 179 207 doi 10 1023 A 1006289418660 e Gombosi T I D L De Zeeuw R M Haberli and K G Powell 1996 Three dimensional multiscale MHD model of cometary plasma environments J Geophys Res 101 15233 15253 The magnetohydrodynamics MHD treats the cometary plasma environment in the fluid approximation using the global 3D magnetohydrodynamic MHD code BATSRUS Block Adaptive Tree Solarwind Roe Type Upwind Scheme The code solves the governing equations of ideal magnetohydrodynamics In the MHD limit the plasma is treated as a single species plasma Effects related to finite gyroradius resistivity and other kinetic effects are neglected However we are able to describe some non MHD effects by describing these deviations from ideal MHD sources and sinks of mass momentum and energy or resistive and d
51. written into the directory listed in the ICES c pl command A unique output file is created for the output from each model selected Output files are named with the name of the model followed by the name of the data input file case used A typical list of output files might be DSMC_CG_1 3_au_00 CO dat DSMC CG 1 3 au 00 C02 dat DSMC CG 1 3 00 Dust dat DSMC 1 3 au 00 H20 dat Electron CG 1 3 au 00 dat Hybrid CG 1 3 au 00 dat MHD CG 1 3 00 dat Most output files have similar formats DSMC Hybrid MHD In these files interpolated values follow the HSTART line the file Above this line is header information which may be unique the model In each file there will be a list of variables in the following format VARIABLES Status X Y Z n Vx Vy Vz Bx By Bz There may be additional information in the header as well Each quantity is listed in a column The status variable is used to indicate errors in the processing Possible values for this quantity are Status Value Meaning 0 Value is fine 1 Position of point was outside the simulation domain Additional values may be added in the future The format for the electron model output is quite different than the other models due to number of data values at each location The format of the file is described below 3 1 ICES C PL AND COMA MODELS 23 MHD MHD output files contain the standard MHD variables Variable Physical Quantity Status Indicates the validi
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