Installing SWMF SWMF/Config.pl WARNING:: no SWMF_data was found make: Nothing to be done for 'install'. VERSION cd CON; make install make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CON' cd Control/src; cp show_git_info.h.orig show_git_info.h make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CON' Installing EE/BATSRUS/ Installing BATSRUS as EE component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/EE/BATSRUS' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/EE/BATSRUS' Installing GM/BATSRUS/ Installing BATSRUS as GM component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS' cp -f srcBATL/BATL_size_orig.f90 srcBATL/BATL_size.f90 cd src; make install make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/src' cp ../srcEquation/ModEquationMhd.f90 ModEquation.f90 cp ModUserDefault.f90 ModUser.f90 cp show_git_info.h.orig show_git_info.h cp ModOptimizeParam_orig.f90 ModOptimizeParam.f90 cp -f ModHdf5_empty.f90 ModHdf5.f90 cp -f ModImplHypre_empty.f90 ModImplHypre.f90 make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS' Installing IE/Ridley_serial/ Installing Ridley_serial as IE component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Ridley_serial' cp -f src/ModSize_orig.f90 src/ModSize.f90 make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Ridley_serial' Installing IH/BATSRUS/ Installing BATSRUS as IH component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IH/BATSRUS' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IH/BATSRUS' Installing IM/CIMI/ Installing CIMI as IM component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI' ./Config.pl -EarthHO -GridDefault make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI' Installing IM/HEIDI/ Installing HEIDI as IM component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/HEIDI' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/HEIDI' Installing IM/RCM2/ Installing RCM2 as IM component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/RCM2' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/RCM2' Installing OH/BATSRUS/ Installing BATSRUS as OH component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/OH/BATSRUS' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/OH/BATSRUS' Installing PC/ALTOR/ Cloning into 'srcBATL_orig'... Installing ALTOR as PC component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR' cp -f src/PC_ModSize_orig.f90 src/PC_ModSize.f90 rm -rf srcBATL; mkdir srcBATL cd srcBATL_orig; cp BATL*.f90 Makefile* ../srcBATL; \ cd ../srcBATL; /homedata/gtoth/SWMFTEST/SWMF/share/Scripts/Methods.pl PC *.f90; \ /homedata/gtoth/SWMFTEST/SWMF/share/Scripts/Rename.pl -w -r -common=PC *.f90; \ perl -i -pe \ 's/user_specify_region/PC_user_specify_region/' *.f90; \ rm -f *~ Number of files to process=20 Finished 22 replacements in file BATL_amr_criteria.f90 Finished 10 replacements in file BATL_high_order.f90 Finished 14 replacements in file BATL_particles.f90 Finished 17 replacements in file BATL_pass_face.f90 Finished 2 replacements in file BATL_size_orig.f90 Thread 1 finished 65 replacement(s) in 5 file(s) Finished 3 replacements in file BATL_geometry.f90 Finished 40 replacements in file BATL_lib.f90 Finished 27 replacements in file BATL_pass_cell_gpu_parallel.f90 Finished 7 replacements in file BATL_pass_node.f90 Finished 15 replacements in file BATL_tree.f90 Thread 3 finished 92 replacement(s) in 5 file(s) Finished 18 replacements in file BATL_amr.f90 Finished 8 replacements in file BATL_interpolate_amr.f90 Finished 30 replacements in file BATL_pass_cell.f90 Finished 5 replacements in file BATL_pass_face_field.f90 Finished 7 replacements in file BATL_test.f90 Thread 2 finished 68 replacement(s) in 5 file(s) Finished 11 replacements in file BATL_grid.f90 Finished 2 replacements in file BATL_mpi.f90 Finished 27 replacements in file BATL_pass_cell_merge.f90 Finished 13 replacements in file BATL_region.f90 Finished 6 replacements in file BATL_unit_test.f90 Thread 4 finished 59 replacement(s) in 5 file(s) cp -f srcBATL/BATL_size_orig.f90 srcBATL/BATL_size.f90 make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR' Installing PC/FLEKS/ Installing FLEKS as PC component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/FLEKS' mkdir bin cp -f include/Constants.h.orig include/Constants.h make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/FLEKS' FLEKS/Config.pl WARNING: could not open ../../util/AMREX/GNUmakefile FLEKS/Config.pl WARNING: could not open ../../util/AMREX/InstallDir/include/AMReX_Config.H Installing PS/DGCPM/ Installing DGCPM as PS component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PS/DGCPM' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PS/DGCPM' Installing PT/AMPS/ Installing AMPS as PT component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS' rm -f output ln -s data/output output AMPS installed make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS' Installing PT/FLEKS/ Installing FLEKS as PC component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/FLEKS' mkdir bin cp -f include/Constants.h.orig include/Constants.h make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/FLEKS' FLEKS/Config.pl WARNING: could not open ../../util/AMREX/GNUmakefile FLEKS/Config.pl WARNING: could not open ../../util/AMREX/InstallDir/include/AMReX_Config.H Installing PT/PARMISAN/ Installing PARMISAN as PT component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/PARMISAN' cp -f src/ModSize_orig.f90 src/ModSize.f90 make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/PARMISAN' Installing PW/PWOM/ Installing PWOM as PW component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM' mkdir bin touch src/Makefile.DEPEND src/Makefile.RULES srcInterface/Makefile.DEPEND srcGITMREADER/Makefile.DEPEND srcGITMREADER/Makefile.RULES srcSTET/Makefile.DEPEND srcSTET/Makefile.RULES srcTWOSTREAM/Makefile.DEPEND srcTWOSTREAM/Makefile.RULES make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM' Installing RB/RBE/ Installing RBE as RB component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/RB/RBE' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/RB/RBE' Installing SC/BATSRUS/ Installing BATSRUS as SC component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SC/BATSRUS' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SC/BATSRUS' Installing SP/MFLAMPA/ Installing MFLAMPA as SP component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SP/MFLAMPA' cp -f src/ModSize_orig.f90 src/ModSize.f90 make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SP/MFLAMPA' Installing UA/GITM/ Installing GITM as UA component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM' cp src/ModSize.f90.orig src/ModSize.f90 touch src/Makefile.DEPEND src/Makefile.RULES srcInterface/Makefile.DEPEND make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM' Configuring GITM for Earth!! Installing UA/GITM2/ Cloning into 'GITM_data'... Updating files: 93% (135/144) Updating files: 94% (136/144) Updating files: 95% (137/144) Updating files: 96% (139/144) Updating files: 97% (140/144) Updating files: 98% (142/144) Updating files: 99% (143/144) Updating files: 100% (144/144) Updating files: 100% (144/144), done. Installing GITM2 as UA component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2' cp src/ModSize.f90.orig src/ModSize.f90 make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2' Configuring GITM for Earth!! Installing UA/MGITM/ srcData is installed in GITM Installing MGITM as UA component make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM' cp src/ModSize.f90.orig src/ModSize.f90 make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM' Configuring GITM for Earth!! Installation succeeded Disabling Hdf5 library in Makefile.conf set_hdf5_: cp GM/BATSRUS/src/ModHdf5_empty.f90 GM/BATSRUS/src/ModHdf5.f90 set_hdf5_: cp share/Library/src/ModHdf5Utils_empty.f90 share/Library/src/ModHdf5Utils.f90 set_spice_: cp share/Library/src/ModSpice_empty.f90 share/Library/src/ModSpice.f90 -rw-rw-r--. 1 gtoth gtoth 1959 Nov 23 19:05 /home/gtoth/Sites/SWMF/gitinfo.txt make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/doc/Tex' rm -f *.out *.aux *.log *.toc *.ind *.idx *.ilg *.dvi *.ps *~ *.protex rm -f SWMFREF.tex SWMFXML.tex SWPC.XML SWPCXML.tex BATSRUS_SCRIPTS.tex rm -f SWMFREF SWMFXML SWPCXML BATSRUS_SCRIPTS cd ..; rm -f SWMF.pdf SWPC.pdf TESTING.pdf MAINTENANCE.pdf PHYSICS.pdf SOFTWARE_STANDARD.pdf make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/doc/Tex' make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/doc/Tex' /homedata/gtoth/SWMFTEST/SWMF/share/Scripts/XmlToTex.pl */PARAM.XML > SWMFXML.tex touch SWMF.ind SWMF.idx pdflatex SWMF.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SWMF.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) Writing index file SWMF.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) No file SWMF.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map} <./SWMF_lo go.png> <./CSEM_logo.pdf>] (../../Copyrights/UM.short) [2] No file SWMF.toc. [3]) (./SWMF_introduction.tex [4] Chapter 1. [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [6] [7] [8] [9] [10] Chapter 2. [11] (../../README.md [12] [13] Underfull \vbox (badness 10000) has occurred while \output is active [14] Underfull \vbox (badness 10000) has occurred while \output is active [15]) [16] [17] [18] [19] LaTeX Warning: Reference `chapter:basics' on page 20 undefined on input line 75 9. LaTeX Warning: Reference `chapter:examples' on page 20 undefined on input line 762. ) [20] Chapter 3. (./SWMF_configuration.tex [21] [22] [23] [24]) (./SWMF_param.tex [25] [26] [27] [28] LaTeX Warning: Reference `chapter:commands' on page 29 undefined on input line 326. [29] [30] Underfull \vbox (badness 10000) has occurred while \output is active [31]) (./SWMF_control.tex [32] [33] [34] [35] [36] [37] [38]) [39] [40] Chapter 4. Overfull \hbox (2.93802pt too wide) in paragraph at lines 38--43 \OT1/cmr/m/n/10 The con-tent of this chap-ter is gen-er-ated from the PARAM.XML file of the CON mod-ule and the PARAM.XML (./SWMFXML.tex [41] [42] [43] [44] [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 458--460 Underfull \hbox (badness 10000) in paragraph at lines 461--467 Underfull \hbox (badness 10000) in paragraph at lines 468--472 [47] [48] [49] [50] Overfull \hbox (39.35724pt too wide) in paragraph at lines 786--794 \OT1/cmr/m/n/10 cou-pling oc-curs from Name-Comp1 to Name-Comp2 af-ter the ini- tial cou-pling, namely when mod(tSimulation,DtCouple) [51] [52] Overfull \hbox (7.11765pt too wide) in paragraph at lines 929--936 \OT1/cmr/m/n/10 Ex-chang-eR-ate lookup ta-ble for two com-po-nents GM and PT fr om an ASCII file OH/Param/ExchangeRate.dat. Overfull \hbox (29.56427pt too wide) in paragraph at lines 929--936 \OT1/cmr/m/n/10 For more com-plete de-scrip-tion, see the #LOOKUPT-ABLE com-man d de-scrip-tion in GM/BATSRUS/PARAM.XML. [53] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (109.52371pt too wide) in paragraph at lines 1592--1595 []\OT1/cmr/m/n/10 The Tol-er-ance pa-ram-e-ter sets if the it-er-a-tive so-lu-t ion Witer is close enough to W, abs(W-Witer).le.Tolerance*[abs(W)+abs(Witer)], [62] [63] [64] [65] [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 2111--2118 [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Overfull \hbox (2.74089pt too wide) in paragraph at lines 2907--2907 [] \OT1/cmtt/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (13.2408pt too wide) in paragraph at lines 2907--2907 []\OT1/cmtt/m/n/10 none - do not change ghost cells. This is useful if the outer boundary is not used.[] [79] Overfull \hbox (2.74089pt too wide) in paragraph at lines 2983--2983 [] \OT1/cmtt/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] [80] [81] Overfull \hbox (18.49075pt too wide) in paragraph at lines 3129--3129 []\OT1/cmtt/m/n/10 'outflow' - same as 'float' but the pressure is set to pOutflow from #OUTFLOWPRESSURE[] [82] Overfull \hbox (60.49039pt too wide) in paragraph at lines 3129--3129 [] \OT1/cmtt/m/n/10 is applied above 55 degrees latitude. S ee #OUTFLOWCRITERIA for more information.[] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 4209--4212 [97] [98] [99] [100] [101] [102] Overfull \hbox (12.7169pt too wide) in paragraph at lines 4658--4665 \OT1/cmr/m/n/10 DIR/octree.rst and an ASCII header file is pro-duced with times tep and time info: RESTARTOUT-DIR/restart.H [103] [104] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4789--4789 [] \OT1/cmtt/m/n/10 none - there will be no indication of time in the logfile (not even the number of steps)[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 2011-02-01T00:00:00 UT StringStartTimeTraj ! Read if String Satellite contains 'trajrange'[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 2011-02-10T00:00:00 UT StringEndTimeTraj ! Read if String Satellite contains 'trajrange'[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 1 h StringDtTraj ! Read if String Satellite contains 'trajrange'[] [105] [106] Overfull \hbox (7.99084pt too wide) in paragraph at lines 4959--4959 [] \OT1/cmtt/m/n/10 Any number followed by ' w'/' d'/' h'/' m'/' s', in which c ase the time is with respect to[] [107] [108] [109] [110] [111] [112] Underfull \vbox (badness 10000) has occurred while \output is active [113] Underfull \vbox (badness 10000) has occurred while \output is active [114] Underfull \vbox (badness 10000) has occurred while \output is active [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] [117] [118] Overfull \hbox (13.2408pt too wide) in paragraph at lines 5686--5686 [] \OT1/cmtt/m/n/10 'eqb' - vars: z PrimVarMinB rCurve xZ0 yZ0 zZ0 PrimVarZ0 rC urveZ0 (B is in SM coordinates)[] Overfull \hbox (23.7407pt too wide) in paragraph at lines 5686--5686 [] \OT1/cmtt/m/n/10 'lgq' - vars: squash.03 squash.12 squash.2 squash-15 squash -2 squash-3 (PlotArea='los' only)[] [119] Overfull \hbox (81.4902pt too wide) in paragraph at lines 5709--5709 [] \OT1/cmtt/m/n/10 DxSavePlot if PlotForm is 'idl' and PlotArea i s not box/shl/sln/slg/shk/los/rfr/lin/eqr/eqb[] [120] Overfull \hbox (10.81253pt too wide) in paragraph at lines 5830--5832 \OT1/cmr/m/n/10 The pos-si-ble val-ues for NameVars with PlotArea 'los' are lis ted in sub-rou-tine set[]plotvar[]los in write[]plot[]los.f90. [121] Overfull \hbox (20.90701pt too wide) in paragraph at lines 5856--5863 \OT1/cmr/m/n/10 The pos-si-ble val-ues for NameVars for other plot ar-eas are l isted in sub-rou-tine set[]plotvar in write[]plot[]common.f90. Underfull \hbox (badness 10000) in paragraph at lines 5864--5873 [122] [123] [124] [125] [126] [127] Overfull \hbox (17.69278pt too wide) in paragraph at lines 6315--6317 []\OT1/cmr/m/n/10 1. RESCALE the data for Cur-rent[A] as fol-lows: Bc-Tube-Dim[ Gs] = 2.0E-03*cPi*Current[A]/RadiusMajor[m] [128] [129] [130] [131] [132] [133] Overfull \hbox (83.3478pt too wide) in paragraph at lines 6717--6723 \OT1/cmr/m/n/10 tial res-o-lu-tion/level still has to be set by this com-mand. How-ever, if #AM-R-CRI-TE-RI-ALEVEL/AMRCRITERIARESOLUTION [134] [135] [136] [137] Overfull \hbox (3.82924pt too wide) in paragraph at lines 7044--7053 \OT1/cmr/m/n/10 are given ei-ther as grid level (for Type-Cri-te-ria="level") o r as grid res-o-lu-tion (for Type-Cri-te-ria="dx/dr/dphi"). [138] [139] [140] Overfull \hbox (0.9391pt too wide) in paragraph at lines 7203--7205 []\OT1/cmr/m/n/10 NOTE 2: the time dis-cretiza-tion scheme can be mod-i-fied wi th the #TIMESTEP-PING, #RUNGEKUTTA [141] [142] [143] [144] Overfull \hbox (14.85689pt too wide) in paragraph at lines 7507--7509 []\OT1/cmr/m/n/10 Note that this com-mand is only ef-fec-tive if the time step con-trol is switched on by th #CON-TROLTIMESTEP [145] [146] Overfull \hbox (37.61134pt too wide) in paragraph at lines 7687--7690 []\OT1/cmr/m/n/10 When Us-eSin-gleIon-Ve-loc-ity is true, the ion ve-loc-i-ties are set to the av-er-age fluid ve-loc-ity $\OML/cmm/m/it/10 u \OT1/cmr/m/n/10 = [] []\OML/cmm/m/it/10 s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]su[]s\OT1/cmr/m /n/10 )\OML/cmm/m/it/10 = [] []s^^Z[]s$ [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] Overfull \hbox (10.50061pt too wide) in paragraph at lines 9620--9622 \OT1/cmr/m/n/10 Fully ion-ized hy-dro-gen plasma is as-sumed. The Coulomb log-a -rithm can be mod-i-fied with the #COULOMBLOG [173] [174] [175] [176] [177] [178] [179] [180] Overfull \hbox (37.16263pt too wide) in paragraph at lines 10262--10268 []\OT1/cmr/m/n/10 On the other hand, the phys-i-cal length of "bad" lines, whic h may be as long as 2*DsThread-Min*nPointThreadMax, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 10000) in paragraph at lines 10876--10893 [191] [192] [193] [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 11305--11314 [196] Underfull \hbox (badness 10000) in paragraph at lines 11315--11316 Underfull \hbox (badness 10000) in paragraph at lines 11333--11341 Underfull \hbox (badness 10000) in paragraph at lines 11342--11343 Overfull \hbox (0.18108pt too wide) in paragraph at lines 11378--11382 \OT1/cmr/m/n/10 Specifies the spa-tial ad-vec-tion scheme. If iOrder-Lat = 7 an d iOrder-Lon = 7, then con-struct lat-i-tude/longitude Underfull \hbox (badness 10000) in paragraph at lines 11386--11387 [197] [198] [199] Overfull \hbox (59.96716pt too wide) in paragraph at lines 11575--11578 []\OT1/cmr/m/n/10 Command tells CIMI to use the KP,AP,F107 val-ues from https:/ /www.gfz-potsdam.de/en/section/geomagnetism/data- [200] [201] Overfull \hbox (44.74052pt too wide) in paragraph at lines 11694--11694 []\OT1/cmtt/m/n/10 `both' or `all' - Output calculated VARIABLES at bot h the ionospher and minimum B surface.[] [202] [203] [204] [205] [206] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 207 [207] [208] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 209 [209] Overfull \hbox (154.98956pt too wide) in paragraph at lines 12278--12278 []\OT1/cmtt/m/n/10 Set DoSaveDifferentialNumberFlux to false to save the distri bution function as opposed to the differential number flux.[] [210] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 211 [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 12494--12495 [213] [214] [215] [216] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 217 [217] Overfull \hbox (338.73796pt too wide) in paragraph at lines 12766--12766 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 u xS1 uyS1 uzS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXY S1 pXZS1 pYZS1'[] Overfull \hbox (118.23988pt too wide) in paragraph at lines 12766--12766 [] \OT1/cmtt/m/n/10 'Bx By Bz Ex Ey Ez ppcS* rhoS* uxS* uyS* uzS* p S* pXXS* pYYS* pZZS* pXYS* pXZS* pYZS* qc divEc dx',[] Overfull \hbox (43.19064pt too wide) in paragraph at lines 12775--12782 \OT1/cmr/m/n/10 (https://public.kitware.com/pipermail/paraview/2013-October/029 492.html https://discourse.paraview.org/t/amrex- [218] Overfull \hbox (3.87921pt too wide) in paragraph at lines 12871--12872 \OT1/cmr/m/n/10 alias="PARTICLETRACKER[]FLEKS0,PARTICLETRACKER[]FLEKS1,PARTICLE TRACKER[]FLEKS2" Overfull \hbox (256.34668pt too wide) in paragraph at lines 12881--12882 \OT1/cmr/m/n/10 alias="TIMESTEPPING[]FLEKS0,TIMESTEPPING[]FLEKS1,TIMESTEP,TIMES TEP[]FLEKS2,TIMESTEP[]FLEKS0,TIMESTEP[]FLEKS1,TIMESTEP[]FLEKS2" Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 219 [219] Overfull \hbox (170.5463pt too wide) in paragraph at lines 12908--12909 \OT1/cmr/m/n/10 alias="RANDOMPARTICLESLOCATION[]FLEKS0,RANDOMPARTICLESLOCATION[ ]FLEKS1,RANDOMPARTICLESLOCATION[]FLEKS2" [220] Overfull \hbox (36.05145pt too wide) in paragraph at lines 13012--13016 \OT1/cmr/m/n/10 For par-ti-cle split-ting and re-sam-pling, the base par-ti-cle num-ber per cell of the level iLev is set to n0*(pLevRatio**iLev), Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 221 [221] [222] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 223 [223] [224] Overfull \hbox (48.87944pt too wide) in paragraph at lines 13284--13285 \OT1/cmr/m/n/10 alias="ADAPTIVESOURCEPPC[]FLEKS0,ADAPTIVESOURCEPPC[]FLEKS1,ADAP TIVESOURCEPPC[]FLEKS2" Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 225 [225] [226] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 227 [227] [228] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 229 [229] [230] [231] [232] [233] Overfull \hbox (459.48691pt too wide) in paragraph at lines 13880--13880 [] \OT1/cmtt/m/n/10 x=x0 - a 2D cut of x=x0 plane. 'x0' is the coordinate. y=y0 - a 2D cut of y=y0 plane. 'y0' is the coordinate. z=z0 - a 2D cut of z=z0 plane. 'z0' is the coordinate. Overfull \hbox (7.99084pt too wide) in paragraph at lines 13888--13888 []\OT1/cmtt/m/n/10 all - all the PIC field vari ables of the first two species:[] Overfull \hbox (18.49075pt too wide) in paragraph at lines 13888--13888 []\OT1/cmtt/m/n/10 fluid - all the FLUID field va riables of the first two species:[] Overfull \hbox (286.23842pt too wide) in paragraph at lines 13888--13888 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 uxS1 uyS1 u zS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXYS1 pXZS1 p YZS1'[] Overfull \hbox (511.98645pt too wide) in paragraph at lines 13900--13900 []\OT1/cmtt/m/n/10 PLANETARY - planetary unit. B field is in nT, velocity is in km/s, length is in planet radius, density is in amu/cm^3, pressure is in nPa. Current and electric field are not well defined.[] [234] [235] Overfull \hbox (28.33832pt too wide) in paragraph at lines 14027--14028 \OT1/cmr/m/n/10 The ca-dence be-tween start-ing sam-pled pro-ce-dure for out-pu t AMPS' data file. #SAM-PLING[]OUTPUT[]CADENCE [236] [237] [238] Overfull \hbox (338.73796pt too wide) in paragraph at lines 14135--14135 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 u xS1 uyS1 uzS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXY S1 pXZS1 pYZS1'[] Overfull \hbox (118.23988pt too wide) in paragraph at lines 14135--14135 [] \OT1/cmtt/m/n/10 'Bx By Bz Ex Ey Ez ppcS* rhoS* uxS* uyS* uzS* p S* pXXS* pYYS* pZZS* pXYS* pXZS* pYZS* qc divEc dx',[] Overfull \hbox (43.19064pt too wide) in paragraph at lines 14144--14151 \OT1/cmr/m/n/10 (https://public.kitware.com/pipermail/paraview/2013-October/029 492.html https://discourse.paraview.org/t/amrex- Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 239 [239] Overfull \hbox (3.87921pt too wide) in paragraph at lines 14240--14241 \OT1/cmr/m/n/10 alias="PARTICLETRACKER[]FLEKS0,PARTICLETRACKER[]FLEKS1,PARTICLE TRACKER[]FLEKS2" Overfull \hbox (256.34668pt too wide) in paragraph at lines 14250--14251 \OT1/cmr/m/n/10 alias="TIMESTEPPING[]FLEKS0,TIMESTEPPING[]FLEKS1,TIMESTEP,TIMES TEP[]FLEKS2,TIMESTEP[]FLEKS0,TIMESTEP[]FLEKS1,TIMESTEP[]FLEKS2" [240] Overfull \hbox (170.5463pt too wide) in paragraph at lines 14277--14278 \OT1/cmr/m/n/10 alias="RANDOMPARTICLESLOCATION[]FLEKS0,RANDOMPARTICLESLOCATION[ ]FLEKS1,RANDOMPARTICLESLOCATION[]FLEKS2" Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 241 [241] Overfull \hbox (36.05145pt too wide) in paragraph at lines 14381--14385 \OT1/cmr/m/n/10 For par-ti-cle split-ting and re-sam-pling, the base par-ti-cle num-ber per cell of the level iLev is set to n0*(pLevRatio**iLev), [242] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 243 [243] [244] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 245 [245] Overfull \hbox (48.87944pt too wide) in paragraph at lines 14653--14654 \OT1/cmr/m/n/10 alias="ADAPTIVESOURCEPPC[]FLEKS0,ADAPTIVESOURCEPPC[]FLEKS1,ADAP TIVESOURCEPPC[]FLEKS2" [246] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 247 [247] [248] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 249 [249] [250] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 251 [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] Overfull \hbox (8.9404pt too wide) in paragraph at lines 16957--16963 \OT1/cmr/m/n/10 These pa-ram-e-ters are used to iden-tify the shock lo-ca-tion: we use iShock-nShockWidth+1:iShock+nShockWidth [279] [280] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] [281] [282] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 283 [283] [284] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 285 [285] [286] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 287 [287] [288] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 289 [289] [290] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 291 [291] [292] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 293 [293] [294] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 295 [295] [296]) (./SWMF.ind) (./SWMF.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on SWMF.pdf (296 pages, 942019 bytes). Transcript written on SWMF.log. makeindex SWMF.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file SWMF.idx....done (803 entries accepted, 0 rejected). Sorting entries.........done (7829 comparisons). Generating output file SWMF.ind....done (840 lines written, 0 warnings). Output written in SWMF.ind. Transcript written in SWMF.ilg. pdflatex SWMF.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SWMF.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) Writing index file SWMF.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./SWMF.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map} <./SWMF_lo go.png> <./CSEM_logo.pdf>] (../../Copyrights/UM.short) [2] (./SWMF.toc [3] [4] [5]) [6]) (./SWMF_introduction.tex Chapter 1. [7] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [8] [9] [10] [11] [12] Chapter 2. [13] (../../README.md [14] [15] Underfull \vbox (badness 10000) has occurred while \output is active [16] Underfull \vbox (badness 10000) has occurred while \output is active [17]) [18] [19] [20] [21] LaTeX Warning: Reference `chapter:examples' on page 22 undefined on input line 762. ) [22] Chapter 3. (./SWMF_configuration.tex [23] [24] [25] [26]) (./SWMF_param.tex [27] [28] [29] [30] [31] [32] Underfull \vbox (badness 10000) has occurred while \output is active [33]) (./SWMF_control.tex [34] [35] [36] [37] [38] [39] [40]) [41] [42] Chapter 4. Overfull \hbox (2.93802pt too wide) in paragraph at lines 38--43 \OT1/cmr/m/n/10 The con-tent of this chap-ter is gen-er-ated from the PARAM.XML file of the CON mod-ule and the PARAM.XML (./SWMFXML.tex [43] [44] [45] [46] [47] [48] Underfull \hbox (badness 10000) in paragraph at lines 458--460 Underfull \hbox (badness 10000) in paragraph at lines 461--467 Underfull \hbox (badness 10000) in paragraph at lines 468--472 [49] [50] [51] [52] Overfull \hbox (39.35724pt too wide) in paragraph at lines 786--794 \OT1/cmr/m/n/10 cou-pling oc-curs from Name-Comp1 to Name-Comp2 af-ter the ini- tial cou-pling, namely when mod(tSimulation,DtCouple) [53] [54] Overfull \hbox (7.11765pt too wide) in paragraph at lines 929--936 \OT1/cmr/m/n/10 Ex-chang-eR-ate lookup ta-ble for two com-po-nents GM and PT fr om an ASCII file OH/Param/ExchangeRate.dat. Overfull \hbox (29.56427pt too wide) in paragraph at lines 929--936 \OT1/cmr/m/n/10 For more com-plete de-scrip-tion, see the #LOOKUPT-ABLE com-man d de-scrip-tion in GM/BATSRUS/PARAM.XML. [55] [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (109.52371pt too wide) in paragraph at lines 1592--1595 []\OT1/cmr/m/n/10 The Tol-er-ance pa-ram-e-ter sets if the it-er-a-tive so-lu-t ion Witer is close enough to W, abs(W-Witer).le.Tolerance*[abs(W)+abs(Witer)], [64] [65] [66] [67] [68] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 2111--2118 [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] Overfull \hbox (2.74089pt too wide) in paragraph at lines 2907--2907 [] \OT1/cmtt/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (13.2408pt too wide) in paragraph at lines 2907--2907 []\OT1/cmtt/m/n/10 none - do not change ghost cells. This is useful if the outer boundary is not used.[] [81] Overfull \hbox (2.74089pt too wide) in paragraph at lines 2983--2983 [] \OT1/cmtt/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] [82] [83] Overfull \hbox (18.49075pt too wide) in paragraph at lines 3129--3129 []\OT1/cmtt/m/n/10 'outflow' - same as 'float' but the pressure is set to pOutflow from #OUTFLOWPRESSURE[] [84] Overfull \hbox (60.49039pt too wide) in paragraph at lines 3129--3129 [] \OT1/cmtt/m/n/10 is applied above 55 degrees latitude. S ee #OUTFLOWCRITERIA for more information.[] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 4209--4212 [99] [100] [101] [102] [103] [104] Overfull \hbox (12.7169pt too wide) in paragraph at lines 4658--4665 \OT1/cmr/m/n/10 DIR/octree.rst and an ASCII header file is pro-duced with times tep and time info: RESTARTOUT-DIR/restart.H [105] [106] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4789--4789 [] \OT1/cmtt/m/n/10 none - there will be no indication of time in the logfile (not even the number of steps)[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 2011-02-01T00:00:00 UT StringStartTimeTraj ! Read if String Satellite contains 'trajrange'[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 2011-02-10T00:00:00 UT StringEndTimeTraj ! Read if String Satellite contains 'trajrange'[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 1 h StringDtTraj ! Read if String Satellite contains 'trajrange'[] [107] [108] Overfull \hbox (7.99084pt too wide) in paragraph at lines 4959--4959 [] \OT1/cmtt/m/n/10 Any number followed by ' w'/' d'/' h'/' m'/' s', in which c ase the time is with respect to[] [109] [110] [111] [112] [113] [114] Underfull \vbox (badness 10000) has occurred while \output is active [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] Underfull \vbox (badness 10000) has occurred while \output is active [117] Underfull \vbox (badness 10000) has occurred while \output is active [118] [119] [120] Overfull \hbox (13.2408pt too wide) in paragraph at lines 5686--5686 [] \OT1/cmtt/m/n/10 'eqb' - vars: z PrimVarMinB rCurve xZ0 yZ0 zZ0 PrimVarZ0 rC urveZ0 (B is in SM coordinates)[] Overfull \hbox (23.7407pt too wide) in paragraph at lines 5686--5686 [] \OT1/cmtt/m/n/10 'lgq' - vars: squash.03 squash.12 squash.2 squash-15 squash -2 squash-3 (PlotArea='los' only)[] [121] Overfull \hbox (81.4902pt too wide) in paragraph at lines 5709--5709 [] \OT1/cmtt/m/n/10 DxSavePlot if PlotForm is 'idl' and PlotArea i s not box/shl/sln/slg/shk/los/rfr/lin/eqr/eqb[] [122] Overfull \hbox (10.81253pt too wide) in paragraph at lines 5830--5832 \OT1/cmr/m/n/10 The pos-si-ble val-ues for NameVars with PlotArea 'los' are lis ted in sub-rou-tine set[]plotvar[]los in write[]plot[]los.f90. [123] Overfull \hbox (20.90701pt too wide) in paragraph at lines 5856--5863 \OT1/cmr/m/n/10 The pos-si-ble val-ues for NameVars for other plot ar-eas are l isted in sub-rou-tine set[]plotvar in write[]plot[]common.f90. Underfull \hbox (badness 10000) in paragraph at lines 5864--5873 [124] [125] [126] [127] [128] [129] Overfull \hbox (17.69278pt too wide) in paragraph at lines 6315--6317 []\OT1/cmr/m/n/10 1. RESCALE the data for Cur-rent[A] as fol-lows: Bc-Tube-Dim[ Gs] = 2.0E-03*cPi*Current[A]/RadiusMajor[m] [130] [131] [132] [133] [134] [135] Overfull \hbox (83.3478pt too wide) in paragraph at lines 6717--6723 \OT1/cmr/m/n/10 tial res-o-lu-tion/level still has to be set by this com-mand. How-ever, if #AM-R-CRI-TE-RI-ALEVEL/AMRCRITERIARESOLUTION [136] [137] [138] [139] Overfull \hbox (3.82924pt too wide) in paragraph at lines 7044--7053 \OT1/cmr/m/n/10 are given ei-ther as grid level (for Type-Cri-te-ria="level") o r as grid res-o-lu-tion (for Type-Cri-te-ria="dx/dr/dphi"). [140] [141] [142] Overfull \hbox (0.9391pt too wide) in paragraph at lines 7203--7205 []\OT1/cmr/m/n/10 NOTE 2: the time dis-cretiza-tion scheme can be mod-i-fied wi th the #TIMESTEP-PING, #RUNGEKUTTA [143] [144] [145] [146] Overfull \hbox (14.85689pt too wide) in paragraph at lines 7507--7509 []\OT1/cmr/m/n/10 Note that this com-mand is only ef-fec-tive if the time step con-trol is switched on by th #CON-TROLTIMESTEP [147] [148] Overfull \hbox (37.61134pt too wide) in paragraph at lines 7687--7690 []\OT1/cmr/m/n/10 When Us-eSin-gleIon-Ve-loc-ity is true, the ion ve-loc-i-ties are set to the av-er-age fluid ve-loc-ity $\OML/cmm/m/it/10 u \OT1/cmr/m/n/10 = [] []\OML/cmm/m/it/10 s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]su[]s\OT1/cmr/m /n/10 )\OML/cmm/m/it/10 = [] []s^^Z[]s$ [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] Overfull \hbox (10.50061pt too wide) in paragraph at lines 9620--9622 \OT1/cmr/m/n/10 Fully ion-ized hy-dro-gen plasma is as-sumed. The Coulomb log-a -rithm can be mod-i-fied with the #COULOMBLOG [175] [176] [177] [178] [179] [180] [181] [182] Overfull \hbox (37.16263pt too wide) in paragraph at lines 10262--10268 []\OT1/cmr/m/n/10 On the other hand, the phys-i-cal length of "bad" lines, whic h may be as long as 2*DsThread-Min*nPointThreadMax, [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] Underfull \hbox (badness 10000) in paragraph at lines 10876--10893 [193] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 11305--11314 [198] Underfull \hbox (badness 10000) in paragraph at lines 11315--11316 Underfull \hbox (badness 10000) in paragraph at lines 11333--11341 Underfull \hbox (badness 10000) in paragraph at lines 11342--11343 Overfull \hbox (0.18108pt too wide) in paragraph at lines 11378--11382 \OT1/cmr/m/n/10 Specifies the spa-tial ad-vec-tion scheme. If iOrder-Lat = 7 an d iOrder-Lon = 7, then con-struct lat-i-tude/longitude Underfull \hbox (badness 10000) in paragraph at lines 11386--11387 [199] [200] [201] Overfull \hbox (59.96716pt too wide) in paragraph at lines 11575--11578 []\OT1/cmr/m/n/10 Command tells CIMI to use the KP,AP,F107 val-ues from https:/ /www.gfz-potsdam.de/en/section/geomagnetism/data- [202] [203] Overfull \hbox (44.74052pt too wide) in paragraph at lines 11694--11694 []\OT1/cmtt/m/n/10 `both' or `all' - Output calculated VARIABLES at bot h the ionospher and minimum B surface.[] [204] [205] [206] [207] [208] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 209 [209] [210] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 211 [211] Overfull \hbox (154.98956pt too wide) in paragraph at lines 12278--12278 []\OT1/cmtt/m/n/10 Set DoSaveDifferentialNumberFlux to false to save the distri bution function as opposed to the differential number flux.[] [212] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 213 [213] [214] Underfull \hbox (badness 10000) in paragraph at lines 12494--12495 [215] [216] [217] [218] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 219 [219] Overfull \hbox (338.73796pt too wide) in paragraph at lines 12766--12766 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 u xS1 uyS1 uzS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXY S1 pXZS1 pYZS1'[] Overfull \hbox (118.23988pt too wide) in paragraph at lines 12766--12766 [] \OT1/cmtt/m/n/10 'Bx By Bz Ex Ey Ez ppcS* rhoS* uxS* uyS* uzS* p S* pXXS* pYYS* pZZS* pXYS* pXZS* pYZS* qc divEc dx',[] Overfull \hbox (43.19064pt too wide) in paragraph at lines 12775--12782 \OT1/cmr/m/n/10 (https://public.kitware.com/pipermail/paraview/2013-October/029 492.html https://discourse.paraview.org/t/amrex- [220] Overfull \hbox (3.87921pt too wide) in paragraph at lines 12871--12872 \OT1/cmr/m/n/10 alias="PARTICLETRACKER[]FLEKS0,PARTICLETRACKER[]FLEKS1,PARTICLE TRACKER[]FLEKS2" Overfull \hbox (256.34668pt too wide) in paragraph at lines 12881--12882 \OT1/cmr/m/n/10 alias="TIMESTEPPING[]FLEKS0,TIMESTEPPING[]FLEKS1,TIMESTEP,TIMES TEP[]FLEKS2,TIMESTEP[]FLEKS0,TIMESTEP[]FLEKS1,TIMESTEP[]FLEKS2" Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 221 [221] Overfull \hbox (170.5463pt too wide) in paragraph at lines 12908--12909 \OT1/cmr/m/n/10 alias="RANDOMPARTICLESLOCATION[]FLEKS0,RANDOMPARTICLESLOCATION[ ]FLEKS1,RANDOMPARTICLESLOCATION[]FLEKS2" [222] Overfull \hbox (36.05145pt too wide) in paragraph at lines 13012--13016 \OT1/cmr/m/n/10 For par-ti-cle split-ting and re-sam-pling, the base par-ti-cle num-ber per cell of the level iLev is set to n0*(pLevRatio**iLev), Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 223 [223] [224] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 225 [225] [226] Overfull \hbox (48.87944pt too wide) in paragraph at lines 13284--13285 \OT1/cmr/m/n/10 alias="ADAPTIVESOURCEPPC[]FLEKS0,ADAPTIVESOURCEPPC[]FLEKS1,ADAP TIVESOURCEPPC[]FLEKS2" Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 227 [227] [228] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 229 [229] [230] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 231 [231] [232] [233] [234] [235] Overfull \hbox (459.48691pt too wide) in paragraph at lines 13880--13880 [] \OT1/cmtt/m/n/10 x=x0 - a 2D cut of x=x0 plane. 'x0' is the coordinate. y=y0 - a 2D cut of y=y0 plane. 'y0' is the coordinate. z=z0 - a 2D cut of z=z0 plane. 'z0' is the coordinate. Overfull \hbox (7.99084pt too wide) in paragraph at lines 13888--13888 []\OT1/cmtt/m/n/10 all - all the PIC field vari ables of the first two species:[] Overfull \hbox (18.49075pt too wide) in paragraph at lines 13888--13888 []\OT1/cmtt/m/n/10 fluid - all the FLUID field va riables of the first two species:[] Overfull \hbox (286.23842pt too wide) in paragraph at lines 13888--13888 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 uxS1 uyS1 u zS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXYS1 pXZS1 p YZS1'[] Overfull \hbox (511.98645pt too wide) in paragraph at lines 13900--13900 []\OT1/cmtt/m/n/10 PLANETARY - planetary unit. B field is in nT, velocity is in km/s, length is in planet radius, density is in amu/cm^3, pressure is in nPa. Current and electric field are not well defined.[] [236] [237] Overfull \hbox (28.33832pt too wide) in paragraph at lines 14027--14028 \OT1/cmr/m/n/10 The ca-dence be-tween start-ing sam-pled pro-ce-dure for out-pu t AMPS' data file. #SAM-PLING[]OUTPUT[]CADENCE [238] [239] [240] Overfull \hbox (338.73796pt too wide) in paragraph at lines 14135--14135 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 u xS1 uyS1 uzS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXY S1 pXZS1 pYZS1'[] Overfull \hbox (118.23988pt too wide) in paragraph at lines 14135--14135 [] \OT1/cmtt/m/n/10 'Bx By Bz Ex Ey Ez ppcS* rhoS* uxS* uyS* uzS* p S* pXXS* pYYS* pZZS* pXYS* pXZS* pYZS* qc divEc dx',[] Overfull \hbox (43.19064pt too wide) in paragraph at lines 14144--14151 \OT1/cmr/m/n/10 (https://public.kitware.com/pipermail/paraview/2013-October/029 492.html https://discourse.paraview.org/t/amrex- Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 241 [241] Overfull \hbox (3.87921pt too wide) in paragraph at lines 14240--14241 \OT1/cmr/m/n/10 alias="PARTICLETRACKER[]FLEKS0,PARTICLETRACKER[]FLEKS1,PARTICLE TRACKER[]FLEKS2" Overfull \hbox (256.34668pt too wide) in paragraph at lines 14250--14251 \OT1/cmr/m/n/10 alias="TIMESTEPPING[]FLEKS0,TIMESTEPPING[]FLEKS1,TIMESTEP,TIMES TEP[]FLEKS2,TIMESTEP[]FLEKS0,TIMESTEP[]FLEKS1,TIMESTEP[]FLEKS2" [242] Overfull \hbox (170.5463pt too wide) in paragraph at lines 14277--14278 \OT1/cmr/m/n/10 alias="RANDOMPARTICLESLOCATION[]FLEKS0,RANDOMPARTICLESLOCATION[ ]FLEKS1,RANDOMPARTICLESLOCATION[]FLEKS2" Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 243 [243] Overfull \hbox (36.05145pt too wide) in paragraph at lines 14381--14385 \OT1/cmr/m/n/10 For par-ti-cle split-ting and re-sam-pling, the base par-ti-cle num-ber per cell of the level iLev is set to n0*(pLevRatio**iLev), [244] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 245 [245] [246] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 247 [247] Overfull \hbox (48.87944pt too wide) in paragraph at lines 14653--14654 \OT1/cmr/m/n/10 alias="ADAPTIVESOURCEPPC[]FLEKS0,ADAPTIVESOURCEPPC[]FLEKS1,ADAP TIVESOURCEPPC[]FLEKS2" [248] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 249 [249] [250] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 251 [251] [252] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 253 [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] Overfull \hbox (8.9404pt too wide) in paragraph at lines 16957--16963 \OT1/cmr/m/n/10 These pa-ram-e-ters are used to iden-tify the shock lo-ca-tion: we use iShock-nShockWidth+1:iShock+nShockWidth [281] [282] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] [283] [284] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 285 [285] [286] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 287 [287] [288] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 289 [289] [290] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 291 [291] [292] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 293 [293] [294] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 295 [295] [296] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 297 [297] [298]) (./SWMF.ind [299] [300] [301] [302] [303] [304] [305] [306] [307]) (./SWMF.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on SWMF.pdf (307 pages, 957813 bytes). Transcript written on SWMF.log. makeindex SWMF.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file SWMF.idx....done (803 entries accepted, 0 rejected). Sorting entries.........done (7829 comparisons). Generating output file SWMF.ind....done (840 lines written, 0 warnings). Output written in SWMF.ind. Transcript written in SWMF.ilg. pdflatex SWMF.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SWMF.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) Writing index file SWMF.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./SWMF.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map} <./SWMF_lo go.png> <./CSEM_logo.pdf>] (../../Copyrights/UM.short) [2] (./SWMF.toc [3] [4] [5]) [6]) (./SWMF_introduction.tex Chapter 1. [7] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [8] [9] [10] [11] [12] Chapter 2. [13] (../../README.md [14] [15] Underfull \vbox (badness 10000) has occurred while \output is active [16] Underfull \vbox (badness 10000) has occurred while \output is active [17]) [18] [19] [20] [21] LaTeX Warning: Reference `chapter:examples' on page 22 undefined on input line 762. ) [22] Chapter 3. (./SWMF_configuration.tex [23] [24] [25] [26]) (./SWMF_param.tex [27] [28] [29] [30] [31] [32] Underfull \vbox (badness 10000) has occurred while \output is active [33]) (./SWMF_control.tex [34] [35] [36] [37] [38] [39] [40]) [41] [42] Chapter 4. Overfull \hbox (2.93802pt too wide) in paragraph at lines 38--43 \OT1/cmr/m/n/10 The con-tent of this chap-ter is gen-er-ated from the PARAM.XML file of the CON mod-ule and the PARAM.XML (./SWMFXML.tex [43] [44] [45] [46] [47] [48] Underfull \hbox (badness 10000) in paragraph at lines 458--460 Underfull \hbox (badness 10000) in paragraph at lines 461--467 Underfull \hbox (badness 10000) in paragraph at lines 468--472 [49] [50] [51] [52] Overfull \hbox (39.35724pt too wide) in paragraph at lines 786--794 \OT1/cmr/m/n/10 cou-pling oc-curs from Name-Comp1 to Name-Comp2 af-ter the ini- tial cou-pling, namely when mod(tSimulation,DtCouple) [53] [54] Overfull \hbox (7.11765pt too wide) in paragraph at lines 929--936 \OT1/cmr/m/n/10 Ex-chang-eR-ate lookup ta-ble for two com-po-nents GM and PT fr om an ASCII file OH/Param/ExchangeRate.dat. Overfull \hbox (29.56427pt too wide) in paragraph at lines 929--936 \OT1/cmr/m/n/10 For more com-plete de-scrip-tion, see the #LOOKUPT-ABLE com-man d de-scrip-tion in GM/BATSRUS/PARAM.XML. [55] [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (109.52371pt too wide) in paragraph at lines 1592--1595 []\OT1/cmr/m/n/10 The Tol-er-ance pa-ram-e-ter sets if the it-er-a-tive so-lu-t ion Witer is close enough to W, abs(W-Witer).le.Tolerance*[abs(W)+abs(Witer)], [64] [65] [66] [67] [68] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 2111--2118 [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] Overfull \hbox (2.74089pt too wide) in paragraph at lines 2907--2907 [] \OT1/cmtt/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (13.2408pt too wide) in paragraph at lines 2907--2907 []\OT1/cmtt/m/n/10 none - do not change ghost cells. This is useful if the outer boundary is not used.[] [81] Overfull \hbox (2.74089pt too wide) in paragraph at lines 2983--2983 [] \OT1/cmtt/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] [82] [83] Overfull \hbox (18.49075pt too wide) in paragraph at lines 3129--3129 []\OT1/cmtt/m/n/10 'outflow' - same as 'float' but the pressure is set to pOutflow from #OUTFLOWPRESSURE[] [84] Overfull \hbox (60.49039pt too wide) in paragraph at lines 3129--3129 [] \OT1/cmtt/m/n/10 is applied above 55 degrees latitude. S ee #OUTFLOWCRITERIA for more information.[] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 4209--4212 [99] [100] [101] [102] [103] [104] Overfull \hbox (12.7169pt too wide) in paragraph at lines 4658--4665 \OT1/cmr/m/n/10 DIR/octree.rst and an ASCII header file is pro-duced with times tep and time info: RESTARTOUT-DIR/restart.H [105] [106] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4789--4789 [] \OT1/cmtt/m/n/10 none - there will be no indication of time in the logfile (not even the number of steps)[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 2011-02-01T00:00:00 UT StringStartTimeTraj ! Read if String Satellite contains 'trajrange'[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 2011-02-10T00:00:00 UT StringEndTimeTraj ! Read if String Satellite contains 'trajrange'[] Overfull \hbox (2.74089pt too wide) in paragraph at lines 4832--4832 []\OT1/cmtt/m/n/10 1 h StringDtTraj ! Read if String Satellite contains 'trajrange'[] [107] [108] Overfull \hbox (7.99084pt too wide) in paragraph at lines 4959--4959 [] \OT1/cmtt/m/n/10 Any number followed by ' w'/' d'/' h'/' m'/' s', in which c ase the time is with respect to[] [109] [110] [111] [112] [113] [114] Underfull \vbox (badness 10000) has occurred while \output is active [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] Underfull \vbox (badness 10000) has occurred while \output is active [117] Underfull \vbox (badness 10000) has occurred while \output is active [118] [119] [120] Overfull \hbox (13.2408pt too wide) in paragraph at lines 5686--5686 [] \OT1/cmtt/m/n/10 'eqb' - vars: z PrimVarMinB rCurve xZ0 yZ0 zZ0 PrimVarZ0 rC urveZ0 (B is in SM coordinates)[] Overfull \hbox (23.7407pt too wide) in paragraph at lines 5686--5686 [] \OT1/cmtt/m/n/10 'lgq' - vars: squash.03 squash.12 squash.2 squash-15 squash -2 squash-3 (PlotArea='los' only)[] [121] Overfull \hbox (81.4902pt too wide) in paragraph at lines 5709--5709 [] \OT1/cmtt/m/n/10 DxSavePlot if PlotForm is 'idl' and PlotArea i s not box/shl/sln/slg/shk/los/rfr/lin/eqr/eqb[] [122] Overfull \hbox (10.81253pt too wide) in paragraph at lines 5830--5832 \OT1/cmr/m/n/10 The pos-si-ble val-ues for NameVars with PlotArea 'los' are lis ted in sub-rou-tine set[]plotvar[]los in write[]plot[]los.f90. [123] Overfull \hbox (20.90701pt too wide) in paragraph at lines 5856--5863 \OT1/cmr/m/n/10 The pos-si-ble val-ues for NameVars for other plot ar-eas are l isted in sub-rou-tine set[]plotvar in write[]plot[]common.f90. Underfull \hbox (badness 10000) in paragraph at lines 5864--5873 [124] [125] [126] [127] [128] [129] Overfull \hbox (17.69278pt too wide) in paragraph at lines 6315--6317 []\OT1/cmr/m/n/10 1. RESCALE the data for Cur-rent[A] as fol-lows: Bc-Tube-Dim[ Gs] = 2.0E-03*cPi*Current[A]/RadiusMajor[m] [130] [131] [132] [133] [134] [135] Overfull \hbox (83.3478pt too wide) in paragraph at lines 6717--6723 \OT1/cmr/m/n/10 tial res-o-lu-tion/level still has to be set by this com-mand. How-ever, if #AM-R-CRI-TE-RI-ALEVEL/AMRCRITERIARESOLUTION [136] [137] [138] [139] Overfull \hbox (3.82924pt too wide) in paragraph at lines 7044--7053 \OT1/cmr/m/n/10 are given ei-ther as grid level (for Type-Cri-te-ria="level") o r as grid res-o-lu-tion (for Type-Cri-te-ria="dx/dr/dphi"). [140] [141] [142] Overfull \hbox (0.9391pt too wide) in paragraph at lines 7203--7205 []\OT1/cmr/m/n/10 NOTE 2: the time dis-cretiza-tion scheme can be mod-i-fied wi th the #TIMESTEP-PING, #RUNGEKUTTA [143] [144] [145] [146] Overfull \hbox (14.85689pt too wide) in paragraph at lines 7507--7509 []\OT1/cmr/m/n/10 Note that this com-mand is only ef-fec-tive if the time step con-trol is switched on by th #CON-TROLTIMESTEP [147] [148] Overfull \hbox (37.61134pt too wide) in paragraph at lines 7687--7690 []\OT1/cmr/m/n/10 When Us-eSin-gleIon-Ve-loc-ity is true, the ion ve-loc-i-ties are set to the av-er-age fluid ve-loc-ity $\OML/cmm/m/it/10 u \OT1/cmr/m/n/10 = [] []\OML/cmm/m/it/10 s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]su[]s\OT1/cmr/m /n/10 )\OML/cmm/m/it/10 = [] []s^^Z[]s$ [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] Overfull \hbox (10.50061pt too wide) in paragraph at lines 9620--9622 \OT1/cmr/m/n/10 Fully ion-ized hy-dro-gen plasma is as-sumed. The Coulomb log-a -rithm can be mod-i-fied with the #COULOMBLOG [175] [176] [177] [178] [179] [180] [181] [182] Overfull \hbox (37.16263pt too wide) in paragraph at lines 10262--10268 []\OT1/cmr/m/n/10 On the other hand, the phys-i-cal length of "bad" lines, whic h may be as long as 2*DsThread-Min*nPointThreadMax, [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] Underfull \hbox (badness 10000) in paragraph at lines 10876--10893 [193] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 11305--11314 [198] Underfull \hbox (badness 10000) in paragraph at lines 11315--11316 Underfull \hbox (badness 10000) in paragraph at lines 11333--11341 Underfull \hbox (badness 10000) in paragraph at lines 11342--11343 Overfull \hbox (0.18108pt too wide) in paragraph at lines 11378--11382 \OT1/cmr/m/n/10 Specifies the spa-tial ad-vec-tion scheme. If iOrder-Lat = 7 an d iOrder-Lon = 7, then con-struct lat-i-tude/longitude Underfull \hbox (badness 10000) in paragraph at lines 11386--11387 [199] [200] [201] Overfull \hbox (59.96716pt too wide) in paragraph at lines 11575--11578 []\OT1/cmr/m/n/10 Command tells CIMI to use the KP,AP,F107 val-ues from https:/ /www.gfz-potsdam.de/en/section/geomagnetism/data- [202] [203] Overfull \hbox (44.74052pt too wide) in paragraph at lines 11694--11694 []\OT1/cmtt/m/n/10 `both' or `all' - Output calculated VARIABLES at bot h the ionospher and minimum B surface.[] [204] [205] [206] [207] [208] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 209 [209] [210] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 211 [211] Overfull \hbox (154.98956pt too wide) in paragraph at lines 12278--12278 []\OT1/cmtt/m/n/10 Set DoSaveDifferentialNumberFlux to false to save the distri bution function as opposed to the differential number flux.[] [212] Overfull \hbox (9.51831pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.5. INPUT COMMANDS FOR THE HOT ELECTRON ION DRIFT INTEGRATOR : IM COMPONENT \OT1/cmr/m/n/10 213 [213] [214] Underfull \hbox (badness 10000) in paragraph at lines 12494--12495 [215] [216] [217] [218] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 219 [219] Overfull \hbox (338.73796pt too wide) in paragraph at lines 12766--12766 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 u xS1 uyS1 uzS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXY S1 pXZS1 pYZS1'[] Overfull \hbox (118.23988pt too wide) in paragraph at lines 12766--12766 [] \OT1/cmtt/m/n/10 'Bx By Bz Ex Ey Ez ppcS* rhoS* uxS* uyS* uzS* p S* pXXS* pYYS* pZZS* pXYS* pXZS* pYZS* qc divEc dx',[] Overfull \hbox (43.19064pt too wide) in paragraph at lines 12775--12782 \OT1/cmr/m/n/10 (https://public.kitware.com/pipermail/paraview/2013-October/029 492.html https://discourse.paraview.org/t/amrex- [220] Overfull \hbox (3.87921pt too wide) in paragraph at lines 12871--12872 \OT1/cmr/m/n/10 alias="PARTICLETRACKER[]FLEKS0,PARTICLETRACKER[]FLEKS1,PARTICLE TRACKER[]FLEKS2" Overfull \hbox (256.34668pt too wide) in paragraph at lines 12881--12882 \OT1/cmr/m/n/10 alias="TIMESTEPPING[]FLEKS0,TIMESTEPPING[]FLEKS1,TIMESTEP,TIMES TEP[]FLEKS2,TIMESTEP[]FLEKS0,TIMESTEP[]FLEKS1,TIMESTEP[]FLEKS2" Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 221 [221] Overfull \hbox (170.5463pt too wide) in paragraph at lines 12908--12909 \OT1/cmr/m/n/10 alias="RANDOMPARTICLESLOCATION[]FLEKS0,RANDOMPARTICLESLOCATION[ ]FLEKS1,RANDOMPARTICLESLOCATION[]FLEKS2" [222] Overfull \hbox (36.05145pt too wide) in paragraph at lines 13012--13016 \OT1/cmr/m/n/10 For par-ti-cle split-ting and re-sam-pling, the base par-ti-cle num-ber per cell of the level iLev is set to n0*(pLevRatio**iLev), Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 223 [223] [224] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 225 [225] [226] Overfull \hbox (48.87944pt too wide) in paragraph at lines 13284--13285 \OT1/cmr/m/n/10 alias="ADAPTIVESOURCEPPC[]FLEKS0,ADAPTIVESOURCEPPC[]FLEKS1,ADAP TIVESOURCEPPC[]FLEKS2" Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 227 [227] [228] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 229 [229] [230] Overfull \hbox (19.58897pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.7. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULAT OR: PC COMPONENT \OT1/cmr/m/n/10 231 [231] [232] [233] [234] [235] Overfull \hbox (459.48691pt too wide) in paragraph at lines 13880--13880 [] \OT1/cmtt/m/n/10 x=x0 - a 2D cut of x=x0 plane. 'x0' is the coordinate. y=y0 - a 2D cut of y=y0 plane. 'y0' is the coordinate. z=z0 - a 2D cut of z=z0 plane. 'z0' is the coordinate. Overfull \hbox (7.99084pt too wide) in paragraph at lines 13888--13888 []\OT1/cmtt/m/n/10 all - all the PIC field vari ables of the first two species:[] Overfull \hbox (18.49075pt too wide) in paragraph at lines 13888--13888 []\OT1/cmtt/m/n/10 fluid - all the FLUID field va riables of the first two species:[] Overfull \hbox (286.23842pt too wide) in paragraph at lines 13888--13888 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 uxS1 uyS1 u zS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXYS1 pXZS1 p YZS1'[] Overfull \hbox (511.98645pt too wide) in paragraph at lines 13900--13900 []\OT1/cmtt/m/n/10 PLANETARY - planetary unit. B field is in nT, velocity is in km/s, length is in planet radius, density is in amu/cm^3, pressure is in nPa. Current and electric field are not well defined.[] [236] [237] Overfull \hbox (28.33832pt too wide) in paragraph at lines 14027--14028 \OT1/cmr/m/n/10 The ca-dence be-tween start-ing sam-pled pro-ce-dure for out-pu t AMPS' data file. #SAM-PLING[]OUTPUT[]CADENCE [238] [239] [240] Overfull \hbox (338.73796pt too wide) in paragraph at lines 14135--14135 [] \OT1/cmtt/m/n/10 'rhoS0 rhoS1 Bx By Bz Ex Ey Ez uxS0 uyS0 uzS0 u xS1 uyS1 uzS1 pS0 pS1 pXXS0 pYYS0 pZZS0 pXYS0 pXZS0 pYZS0 pXXS1 pYYS1 pZZS1 pXY S1 pXZS1 pYZS1'[] Overfull \hbox (118.23988pt too wide) in paragraph at lines 14135--14135 [] \OT1/cmtt/m/n/10 'Bx By Bz Ex Ey Ez ppcS* rhoS* uxS* uyS* uzS* p S* pXXS* pYYS* pZZS* pXYS* pXZS* pYZS* qc divEc dx',[] Overfull \hbox (43.19064pt too wide) in paragraph at lines 14144--14151 \OT1/cmr/m/n/10 (https://public.kitware.com/pipermail/paraview/2013-October/029 492.html https://discourse.paraview.org/t/amrex- Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 241 [241] Overfull \hbox (3.87921pt too wide) in paragraph at lines 14240--14241 \OT1/cmr/m/n/10 alias="PARTICLETRACKER[]FLEKS0,PARTICLETRACKER[]FLEKS1,PARTICLE TRACKER[]FLEKS2" Overfull \hbox (256.34668pt too wide) in paragraph at lines 14250--14251 \OT1/cmr/m/n/10 alias="TIMESTEPPING[]FLEKS0,TIMESTEPPING[]FLEKS1,TIMESTEP,TIMES TEP[]FLEKS2,TIMESTEP[]FLEKS0,TIMESTEP[]FLEKS1,TIMESTEP[]FLEKS2" [242] Overfull \hbox (170.5463pt too wide) in paragraph at lines 14277--14278 \OT1/cmr/m/n/10 alias="RANDOMPARTICLESLOCATION[]FLEKS0,RANDOMPARTICLESLOCATION[ ]FLEKS1,RANDOMPARTICLESLOCATION[]FLEKS2" Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 243 [243] Overfull \hbox (36.05145pt too wide) in paragraph at lines 14381--14385 \OT1/cmr/m/n/10 For par-ti-cle split-ting and re-sam-pling, the base par-ti-cle num-ber per cell of the level iLev is set to n0*(pLevRatio**iLev), [244] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 245 [245] [246] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 247 [247] Overfull \hbox (48.87944pt too wide) in paragraph at lines 14653--14654 \OT1/cmr/m/n/10 alias="ADAPTIVESOURCEPPC[]FLEKS0,ADAPTIVESOURCEPPC[]FLEKS1,ADAP TIVESOURCEPPC[]FLEKS2" [248] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 249 [249] [250] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 251 [251] [252] Overfull \hbox (24.58899pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.10. INPUT COMMANDS FOR THE FLEXIBLE EXASCALE KINETIC SIMULA TOR: PC COMPONENT \OT1/cmr/m/n/10 253 [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] Overfull \hbox (8.9404pt too wide) in paragraph at lines 16957--16963 \OT1/cmr/m/n/10 These pa-ram-e-ters are used to iden-tify the shock lo-ca-tion: we use iShock-nShockWidth+1:iShock+nShockWidth [281] [282] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] Overfull \hbox (49.99048pt too wide) in paragraph at lines 17139--17139 []\OT1/cmtt/m/n/10 215.0 Radius [Rs] (read if mh2d/mh time/distr2d/distrtime/flux2d/fluxtime)[] [283] [284] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 285 [285] [286] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 287 [287] [288] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 289 [289] [290] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.15. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 291 [291] [292] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 293 [293] [294] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 295 [295] [296] Overfull \hbox (58.12965pt too wide) has occurred while \output is active \OT1/cmr/m/sl/10 4.16. INPUT COMMANDS FOR THE GLOBAL IONOSPHERE THERMOSPHERE M ODEL 2: UA COMPONENT \OT1/cmr/m/n/10 297 [297] [298]) (./SWMF.ind [299] [300] [301] [302] [303] [304] [305] [306] [307]) (./SWMF.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information) Output written on SWMF.pdf (307 pages, 958052 bytes). Transcript written on SWMF.log. mv SWMF.pdf ../ rm -f SWMF.ind SWMF.idx SWMF.ilg cd ../..; /homedata/gtoth/SWMFTEST/SWMF/share/Scripts/ParamToXml.pl -o=doc/Tex/SWPC.XML \ Param/SWPC/PARAM.in_SWPC_init \ Param/SWPC/PARAM.in_SWPC_restart /homedata/gtoth/SWMFTEST/SWMF/share/Scripts/XmlToTex.pl SWPC.XML > SWPCXML.tex touch SWPC.ind SWPC.idx pdflatex SWPC.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SWPC.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) Writing index file SWPC.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) No file SWPC.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map} <./SWMF_lo go.png> <./CSEM_logo.pdf>] (../../Copyrights/UM.short) [2] No file SWPC.toc. [3]) (./SWMF_introduction.tex [4] Chapter 1. [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [6] [7] [8] [9] [10] Chapter 2. [11] (../../README.md [12] [13] Underfull \vbox (badness 10000) has occurred while \output is active [14] Underfull \vbox (badness 10000) has occurred while \output is active [15]) [16] [17] [18] [19] LaTeX Warning: Reference `chapter:basics' on page 20 undefined on input line 75 9. LaTeX Warning: Reference `chapter:examples' on page 20 undefined on input line 762. ) [20] Chapter 3. (./SWMF_configuration.tex [21] [22] [23] [24]) (./SWMF_param.tex [25] [26] [27] [28] LaTeX Warning: Reference `chapter:commands' on page 29 undefined on input line 326. [29] [30] Underfull \vbox (badness 10000) has occurred while \output is active [31]) (./SWMF_control.tex [32] [33] [34] [35] [36] [37] [38]) [39] [40] Chapter 4. Overfull \hbox (2.93802pt too wide) in paragraph at lines 34--39 \OT1/cmr/m/n/10 The con-tent of this chap-ter is gen-er-ated from the PARAM.XML file of the CON mod-ule and the PARAM.XML (./SWPCXML.tex [41]) (./SWPC.ind) (./SWPC.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on SWPC.pdf (41 pages, 340923 bytes). Transcript written on SWPC.log. makeindex SWPC.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file SWPC.idx...done (0 entries accepted, 0 rejected). Nothing written in SWPC.ind. Transcript written in SWPC.ilg. pdflatex SWPC.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SWPC.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) Writing index file SWPC.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./SWPC.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map} <./SWMF_lo go.png> <./CSEM_logo.pdf>] (../../Copyrights/UM.short) [2] (./SWPC.toc) [3]) (./SWMF_introduction.tex [4] Chapter 1. [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [6] [7] [8] [9] [10] Chapter 2. [11] (../../README.md [12] [13] Underfull \vbox (badness 10000) has occurred while \output is active [14] Underfull \vbox (badness 10000) has occurred while \output is active [15]) [16] [17] [18] [19] LaTeX Warning: Reference `chapter:examples' on page 20 undefined on input line 762. ) [20] Chapter 3. (./SWMF_configuration.tex [21] [22] [23] [24]) (./SWMF_param.tex [25] [26] [27] [28] [29] [30] Underfull \vbox (badness 10000) has occurred while \output is active [31]) (./SWMF_control.tex [32] [33] [34] [35] [36] [37] [38]) [39] [40] Chapter 4. Overfull \hbox (2.93802pt too wide) in paragraph at lines 34--39 \OT1/cmr/m/n/10 The con-tent of this chap-ter is gen-er-ated from the PARAM.XML file of the CON mod-ule and the PARAM.XML (./SWPCXML.tex [41]) (./SWPC.ind) (./SWPC.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information) Output written on SWPC.pdf (41 pages, 343739 bytes). Transcript written on SWPC.log. makeindex SWPC.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file SWPC.idx...done (0 entries accepted, 0 rejected). Nothing written in SWPC.ind. Transcript written in SWPC.ilg. pdflatex SWPC.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SWPC.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) Writing index file SWPC.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./SWPC.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map} <./SWMF_lo go.png> <./CSEM_logo.pdf>] (../../Copyrights/UM.short) [2] (./SWPC.toc) [3]) (./SWMF_introduction.tex [4] Chapter 1. [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [6] [7] [8] [9] [10] Chapter 2. [11] (../../README.md [12] [13] Underfull \vbox (badness 10000) has occurred while \output is active [14] Underfull \vbox (badness 10000) has occurred while \output is active [15]) [16] [17] [18] [19] LaTeX Warning: Reference `chapter:examples' on page 20 undefined on input line 762. ) [20] Chapter 3. (./SWMF_configuration.tex [21] [22] [23] [24]) (./SWMF_param.tex [25] [26] [27] [28] [29] [30] Underfull \vbox (badness 10000) has occurred while \output is active [31]) (./SWMF_control.tex [32] [33] [34] [35] [36] [37] [38]) [39] [40] Chapter 4. Overfull \hbox (2.93802pt too wide) in paragraph at lines 34--39 \OT1/cmr/m/n/10 The con-tent of this chap-ter is gen-er-ated from the PARAM.XML file of the CON mod-ule and the PARAM.XML (./SWPCXML.tex [41]) (./SWPC.ind) (./SWPC.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information) Output written on SWPC.pdf (41 pages, 343739 bytes). Transcript written on SWPC.log. mv SWPC.pdf ../ rm -f SWPC.ind SWPC.idx SWPC.ilg touch TESTING.ind TESTING.idx pdflatex TESTING.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./TESTING.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) No file TESTING.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] No file TESTING.toc. [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] LaTeX Warning: Reference `sec:portability' on page 4 undefined on input line 12 7. LaTeX Warning: Reference `sec:portability' on page 4 undefined on input line 13 8. [4] [5] (./TESTING.aux) LaTeX Warning: There were undefined references. ) Output written on TESTING.pdf (5 pages, 227166 bytes). Transcript written on TESTING.log. makeindex TESTING.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file TESTING.idx...done (0 entries accepted, 0 rejected). Nothing written in TESTING.ind. Transcript written in TESTING.ilg. pdflatex TESTING.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./TESTING.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./TESTING.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] (./TESTING.toc) [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] LaTeX Warning: Reference `sec:portability' on page 4 undefined on input line 12 7. LaTeX Warning: Reference `sec:portability' on page 4 undefined on input line 13 8. [4] [5] (./TESTING.aux) LaTeX Warning: There were undefined references. ) Output written on TESTING.pdf (5 pages, 232508 bytes). Transcript written on TESTING.log. makeindex TESTING.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file TESTING.idx...done (0 entries accepted, 0 rejected). Nothing written in TESTING.ind. Transcript written in TESTING.ilg. pdflatex TESTING.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./TESTING.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./TESTING.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] (./TESTING.toc) [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] LaTeX Warning: Reference `sec:portability' on page 4 undefined on input line 12 7. LaTeX Warning: Reference `sec:portability' on page 4 undefined on input line 13 8. [4] [5] (./TESTING.aux) LaTeX Warning: There were undefined references. ) Output written on TESTING.pdf (5 pages, 232508 bytes). Transcript written on TESTING.log. mv TESTING.pdf ../ rm -f TESTING.ind TESTING.idx TESTING.ilg touch MAINTENANCE.ind MAINTENANCE.idx pdflatex MAINTENANCE.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./MAINTENANCE.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) No file MAINTENANCE.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] No file MAINTENANCE.toc. [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] Overfull \hbox (47.8331pt too wide) in paragraph at lines 211--214 []\OT1/cmr/m/n/10 Add en-tries for this physics do-main to the \OT1/cmtt/m/n/10 CON[]wrapper.f90 \OT1/cmr/m/n/10 and \OT1/cmtt/m/n/10 CON[]couple[]all.f90 \OT 1/cmr/m/n/10 files in \OT1/cmtt/m/n/10 CON/Interface/src\OT1/cmr/m/n/10 ; Overfull \hbox (22.8828pt too wide) in paragraph at lines 226--228 []\OT1/cmr/m/n/10 Add the new com-po-nent into the $Valid-Comp vari-able in \OT 1/cmtt/m/n/10 Config.pl \OT1/cmr/m/n/10 and in \OT1/cmtt/m/n/10 share/Scripts/C heckParam.pl\OT1/cmr/m/n/10 ; [5] (./PM_wrapper.tex [6] Underfull \hbox (badness 10000) in paragraph at lines 70--71 [7] Underfull \vbox (badness 10000) has occurred while \output is active [8] [9] [10] [11] [12]) [13] (./PM_XY_coupler.tex [14] Underfull \hbox (badness 10000) in paragraph at lines 61--62 [15] Underfull \hbox (badness 10000) in paragraph at lines 123--124 [16] Underfull \hbox (badness 10000) in paragraph at lines 213--214 [17] Underfull \hbox (badness 10000) in paragraph at lines 269--270 [18]) [19] (../RELEASENOTES [20] [21]) [22] (./MAINTENANCE.aux) ) (see the transcript file for additional information) Output written on MAINTENANCE.pdf (22 pages, 286451 bytes). Transcript written on MAINTENANCE.log. makeindex MAINTENANCE.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file MAINTENANCE.idx...done (0 entries accepted, 0 rejected). Nothing written in MAINTENANCE.ind. Transcript written in MAINTENANCE.ilg. pdflatex MAINTENANCE.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./MAINTENANCE.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./MAINTENANCE.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] (./MAINTENANCE.toc) [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] Overfull \hbox (47.8331pt too wide) in paragraph at lines 211--214 []\OT1/cmr/m/n/10 Add en-tries for this physics do-main to the \OT1/cmtt/m/n/10 CON[]wrapper.f90 \OT1/cmr/m/n/10 and \OT1/cmtt/m/n/10 CON[]couple[]all.f90 \OT 1/cmr/m/n/10 files in \OT1/cmtt/m/n/10 CON/Interface/src\OT1/cmr/m/n/10 ; Overfull \hbox (22.8828pt too wide) in paragraph at lines 226--228 []\OT1/cmr/m/n/10 Add the new com-po-nent into the $Valid-Comp vari-able in \OT 1/cmtt/m/n/10 Config.pl \OT1/cmr/m/n/10 and in \OT1/cmtt/m/n/10 share/Scripts/C heckParam.pl\OT1/cmr/m/n/10 ; [5] (./PM_wrapper.tex [6] Underfull \hbox (badness 10000) in paragraph at lines 70--71 [7] Underfull \vbox (badness 10000) has occurred while \output is active [8] [9] [10] [11] [12]) [13] (./PM_XY_coupler.tex [14] Underfull \hbox (badness 10000) in paragraph at lines 61--62 [15] Underfull \hbox (badness 10000) in paragraph at lines 123--124 [16] Underfull \hbox (badness 10000) in paragraph at lines 213--214 [17] Underfull \hbox (badness 10000) in paragraph at lines 269--270 [18]) [19] (../RELEASENOTES [20] [21]) [22] (./MAINTENANCE.aux) ) (see the transcript file for additional information) Output written on MAINTENANCE.pdf (22 pages, 291058 bytes). Transcript written on MAINTENANCE.log. makeindex MAINTENANCE.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file MAINTENANCE.idx...done (0 entries accepted, 0 rejected). Nothing written in MAINTENANCE.ind. Transcript written in MAINTENANCE.ilg. pdflatex MAINTENANCE.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./MAINTENANCE.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./MAINTENANCE.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] (./MAINTENANCE.toc) [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] Overfull \hbox (47.8331pt too wide) in paragraph at lines 211--214 []\OT1/cmr/m/n/10 Add en-tries for this physics do-main to the \OT1/cmtt/m/n/10 CON[]wrapper.f90 \OT1/cmr/m/n/10 and \OT1/cmtt/m/n/10 CON[]couple[]all.f90 \OT 1/cmr/m/n/10 files in \OT1/cmtt/m/n/10 CON/Interface/src\OT1/cmr/m/n/10 ; Overfull \hbox (22.8828pt too wide) in paragraph at lines 226--228 []\OT1/cmr/m/n/10 Add the new com-po-nent into the $Valid-Comp vari-able in \OT 1/cmtt/m/n/10 Config.pl \OT1/cmr/m/n/10 and in \OT1/cmtt/m/n/10 share/Scripts/C heckParam.pl\OT1/cmr/m/n/10 ; [5] (./PM_wrapper.tex [6] Underfull \hbox (badness 10000) in paragraph at lines 70--71 [7] Underfull \vbox (badness 10000) has occurred while \output is active [8] [9] [10] [11] [12]) [13] (./PM_XY_coupler.tex [14] Underfull \hbox (badness 10000) in paragraph at lines 61--62 [15] Underfull \hbox (badness 10000) in paragraph at lines 123--124 [16] Underfull \hbox (badness 10000) in paragraph at lines 213--214 [17] Underfull \hbox (badness 10000) in paragraph at lines 269--270 [18]) [19] (../RELEASENOTES [20] [21]) [22] (./MAINTENANCE.aux) ) (see the transcript file for additional information) Output written on MAINTENANCE.pdf (22 pages, 291058 bytes). Transcript written on MAINTENANCE.log. mv MAINTENANCE.pdf ../ rm -f MAINTENANCE.ind MAINTENANCE.idx MAINTENANCE.ilg touch PHYSICS.ind PHYSICS.idx pdflatex PHYSICS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./PHYSICS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) No file PHYSICS.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] No file PHYSICS.toc. [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) LaTeX Warning: Citation `Groth2000' on page 3 undefined on input line 85. LaTeX Warning: Citation `Usmanov2000' on page 3 undefined on input line 85. LaTeX Warning: Citation `Wu1999' on page 3 undefined on input line 87. LaTeX Warning: Citation `Roussev2003b' on page 3 undefined on input line 89. [3] LaTeX Warning: Citation `Forbes1991' on page 4 undefined on input line 131. LaTeX Warning: Citation `Gibson1998' on page 4 undefined on input line 131. LaTeX Warning: Citation `Roussev2003a' on page 4 undefined on input line 131. LaTeX Warning: Citation `Wu2000' on page 4 undefined on input line 134. LaTeX Warning: Citation `Chen1993' on page 4 undefined on input line 135. LaTeX Warning: Citation `Low2001' on page 4 undefined on input line 136. LaTeX Warning: Citation `Antiochos1999' on page 4 undefined on input line 137. LaTeX Warning: Citation `Manchester2003' on page 4 undefined on input line 137. LaTeX Warning: Citation `Roussev2004' on page 4 undefined on input line 137. [4] LaTeX Warning: Citation `Sokolov2004' on page 5 undefined on input line 179. LaTeX Warning: Citation `Kota1999' on page 5 undefined on input line 180. LaTeX Warning: Citation `Kota2005' on page 5 undefined on input line 180. LaTeX Warning: Citation `DeZeeuw2004' on page 5 undefined on input line 219. LaTeX Warning: Citation `Ebihara2002' on page 5 undefined on input line 239. LaTeX Warning: Citation `Wolf1982' on page 5 undefined on input line 240. LaTeX Warning: Citation `Toffoletto2003' on page 5 undefined on input line 240. LaTeX Warning: Citation `Fok2001' on page 5 undefined on input line 244. LaTeX Warning: Citation `Liemohn2004' on page 5 undefined on input line 245. LaTeX Warning: Citation `Ridley2002' on page 5 undefined on input line 245. LaTeX Warning: Citation `Chen2003' on page 5 undefined on input line 249. LaTeX Warning: Citation `Ebihara2004' on page 5 undefined on input line 249. [5] LaTeX Warning: Citation `Beutier1995' on page 6 undefined on input line 273. LaTeX Warning: Citation `Shprits2004' on page 6 undefined on input line 273. LaTeX Warning: Citation `Elkington1999' on page 6 undefined on input line 274. LaTeX Warning: Citation `Weimer1996' on page 6 undefined on input line 286. LaTeX Warning: Citation `Fuller1987' on page 6 undefined on input line 287. LaTeX Warning: Citation `Richmond1988' on page 6 undefined on input line 289. LaTeX Warning: Citation `Ridley2004' on page 6 undefined on input line 292. LaTeX Warning: Citation `Ridley2002' on page 6 undefined on input line 292. LaTeX Warning: Citation `Robinson1987' on page 6 undefined on input line 304. LaTeX Warning: Citation `Moen1993' on page 6 undefined on input line 304. LaTeX Warning: Citation `Richmond1992' on page 6 undefined on input line 322. LaTeX Warning: Citation `Ridley2005' on page 6 undefined on input line 323. [6] LaTeX Warning: Citation `Toth2005c' on page 7 undefined on input line 354. LaTeX Warning: Citation `Toth2005c' on page 7 undefined on input line 366. [7] [8] Underfull \hbox (badness 2828) in paragraph at lines 530--534 []\OT1/cmr/m/n/10 Ridley, A. J. and M. W. Liemohn (2002), A model-derived storm - [9] [10] (./PHYSICS.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> Output written on PHYSICS.pdf (10 pages, 253979 bytes). Transcript written on PHYSICS.log. makeindex PHYSICS.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file PHYSICS.idx...done (0 entries accepted, 0 rejected). Nothing written in PHYSICS.ind. Transcript written in PHYSICS.ilg. pdflatex PHYSICS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./PHYSICS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./PHYSICS.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] (./PHYSICS.toc) [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] [5] Overfull \hbox (2.65068pt too wide) in paragraph at lines 283--297 \OT1/cmr/m/n/10 cur-rents to cal-cu-late par-ti-cle pre-cip-i-ta-tion and con-d uc-tances [[], []]. [6] [7] [8] Underfull \hbox (badness 2828) in paragraph at lines 530--534 []\OT1/cmr/m/n/10 Ridley, A. J. and M. W. Liemohn (2002), A model-derived storm - [9] [10] (./PHYSICS.aux) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> Output written on PHYSICS.pdf (10 pages, 260067 bytes). Transcript written on PHYSICS.log. makeindex PHYSICS.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file PHYSICS.idx...done (0 entries accepted, 0 rejected). Nothing written in PHYSICS.ind. Transcript written in PHYSICS.ilg. pdflatex PHYSICS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./PHYSICS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (./html.sty) (./PHYSICS.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (../../Copyrights/UM.short) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/u pdmap/pdftex.map} <./SWMF_logo.png> <./CSEM_logo.pdf>] (./PHYSICS.toc) [2]) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] [5] Overfull \hbox (2.65068pt too wide) in paragraph at lines 283--297 \OT1/cmr/m/n/10 cur-rents to cal-cu-late par-ti-cle pre-cip-i-ta-tion and con-d uc-tances [[], []]. [6] [7] [8] Underfull \hbox (badness 2828) in paragraph at lines 530--534 []\OT1/cmr/m/n/10 Ridley, A. J. and M. W. Liemohn (2002), A model-derived storm - [9] [10] (./PHYSICS.aux) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> Output written on PHYSICS.pdf (10 pages, 260067 bytes). Transcript written on PHYSICS.log. mv PHYSICS.pdf ../ rm -f PHYSICS.ind PHYSICS.idx PHYSICS.ilg touch SOFTWARE_STANDARD.ind SOFTWARE_STANDARD.idx pdflatex SOFTWARE_STANDARD.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SOFTWARE_STANDARD.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) No file SOFTWARE_STANDARD.aux. [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] No file SOFTWARE_STANDARD.toc. [2] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] LaTeX Warning: Reference `sec:object' on page 5 undefined on input line 116. [5] [6] [7] [8] [9] [10] Overfull \hbox (59.24648pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_block_lu ! LU preconditioner for up to hep ta block-diagonal[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_upper ! multiply with upper block trian gular matrix[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_lower ! multiply with lower block trian gular matrix[] [11] [12] Overfull \hbox (32.9967pt too wide) in paragraph at lines 547--547 [] \OT1/cmtt/m/n/10 public:: sph_to_xyz ! convert spherical into Cartesian coordinates[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 547--547 [] \OT1/cmtt/m/n/10 module procedure sph_to_xyz11, sph_to_xyz13, sph_to_xyz 31, sph_to_xyz33[] [13] [14] Overfull \hbox (6.74693pt too wide) in paragraph at lines 696--696 [] \OT1/cmtt/m/n/10 if(.not. allocated(Matrix_II)) allocate(Matrix_II(nColumn ,nRow))[] [15] Overfull \hbox (1.49698pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 use BALT_lib, ONLY: MinI, MaxI, MinJ, MaxJ, MinK, MaxK, Ma xBlock[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 !========================================================= ===============[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 allocate(State_VGB(nVar,MinI:MaxI,MinJ:MaxJ,MinK:MaxK,M axBlock))[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 type(StateType):: State_GB(MinI:MaxI,MinJ:MaxJ,MinK:MaxK,M axBlock)[] LaTeX Warning: Reference `sec:named' on page 16 undefined on input line 740. [16] [17] Overfull \hbox (22.4968pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Velocity0 ! the shear velocity far from the s hear layer[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Width ! the width of the layer in the Y d irection[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Perturbation ! the perturbation in the Y compone nt of velocity[] [18] Overfull \hbox (122.24593pt too wide) in paragraph at lines 915--915 [] \OT1/cmtt/m/n/10 write(*,*)'Please provide the x, y and z parameters that de fine the size of the region:'[] LaTeX Warning: Reference `fig:badformat' on page 19 undefined on input line 921 . Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !------------------------------------------------------- ----------------[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] LaTeX Warning: Reference `fig:goodformat' on page 19 undefined on input line 97 5. LaTeX Warning: Reference `fig:nested' on page 19 undefined on input line 980. Overfull \hbox (22.4968pt too wide) in paragraph at lines 1010--1010 [] \OT1/cmtt/m/n/10 Plot_VGB(iPlotVar,i,j,k,iBlock) = State_VGB(Rho_,i,j ,k,iBlock)[] [19] [20] [21] [22] [23] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 Beta ! not specific, beta can be a lot of things[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 nGrid_Points ! difficult to remember, not unique[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 CentripetalForce ! misleading if it is really centrifugal force[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 CristophelCoeff ! pretentious when it simply means face area/dx[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 UseCT ! incomprehensible for non-e xperts[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1127--1127 []\OT1/cmtt/m/n/10 integer:: iMethods ! 1 = Roe scheme, 2 = HLL scheme, 3 = Lax-Friedricsh[] [24] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1127--1127 []\OT1/cmtt/m/n/10 logical:: FirstOrder ! .true. = first order, .false. = s econd order[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1164--1164 []\OT1/cmtt/m/n/10 integer :: nOrder ! 1 = first order, 2 = second order[] [25] Overfull \hbox (11.80951pt too wide) in paragraph at lines 1185--1189 []\OT1/cmr/m/n/10 If a num-ber has to be sin-gle or dou-ble pre-ci-sion, we use the \OT1/cmtt/m/n/10 selected[]real[]kind [26] LaTeX Warning: Reference `tab:components' on page 27 undefined on input line 13 06. [27] Overfull \hbox (32.9967pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 Config.pl configuration script (using share/Script s/Config.pl)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 Makefile with targets install, LIB, rundir, clean , distclean[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 output/ reference solutions of the functionality tests[] [28] [29] [30] [31] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 logical:: DoneComputation ! done with the co mputation[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 logical:: UseConstrainedB ! use constrained transport scheme[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 integer:: MaxBlock ! maximum number o f blocks[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 integer:: MinBoundary ! minimum value of boundary index[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 character(len=20):: TypeFlux ! type of the nume rical flux[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 character(len=100):: StringLogVar ! variables saved into the log file[] Overfull \hbox (17.41568pt too wide) in paragraph at lines 1568--1590 [] LaTeX Warning: Reference `tab:index' on page 32 undefined on input line 1599. [32] [33] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 B0x_XB(:,:,:,:) - real array indexed by the X faces and blocks[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 nRoot_D(:) - integer array indexed by the 3 directi ons (x,y,z)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 Buffer_VII(:,:,:) - real buffer with one variable and two other indexes[] [34] [35] (./SOFTWARE_STANDARD.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on SOFTWARE_STANDARD.pdf (35 pages, 198897 bytes). Transcript written on SOFTWARE_STANDARD.log. makeindex SOFTWARE_STANDARD.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file SOFTWARE_STANDARD.idx...done (0 entries accepted, 0 rejected). Nothing written in SOFTWARE_STANDARD.ind. Transcript written in SOFTWARE_STANDARD.ilg. pdflatex SOFTWARE_STANDARD.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SOFTWARE_STANDARD.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./SOFTWARE_STANDARD.aux) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/upd map/pdftex.map}] (./SOFTWARE_STANDARD.toc) [2] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] [5] [6] [7] [8] [9] [10] Overfull \hbox (59.24648pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_block_lu ! LU preconditioner for up to hep ta block-diagonal[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_upper ! multiply with upper block trian gular matrix[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_lower ! multiply with lower block trian gular matrix[] [11] [12] Overfull \hbox (32.9967pt too wide) in paragraph at lines 547--547 [] \OT1/cmtt/m/n/10 public:: sph_to_xyz ! convert spherical into Cartesian coordinates[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 547--547 [] \OT1/cmtt/m/n/10 module procedure sph_to_xyz11, sph_to_xyz13, sph_to_xyz 31, sph_to_xyz33[] [13] [14] Overfull \hbox (6.74693pt too wide) in paragraph at lines 696--696 [] \OT1/cmtt/m/n/10 if(.not. allocated(Matrix_II)) allocate(Matrix_II(nColumn ,nRow))[] [15] Overfull \hbox (1.49698pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 use BALT_lib, ONLY: MinI, MaxI, MinJ, MaxJ, MinK, MaxK, Ma xBlock[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 !========================================================= ===============[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 allocate(State_VGB(nVar,MinI:MaxI,MinJ:MaxJ,MinK:MaxK,M axBlock))[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 type(StateType):: State_GB(MinI:MaxI,MinJ:MaxJ,MinK:MaxK,M axBlock)[] [16] [17] Overfull \hbox (22.4968pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Velocity0 ! the shear velocity far from the s hear layer[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Width ! the width of the layer in the Y d irection[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Perturbation ! the perturbation in the Y compone nt of velocity[] [18] Overfull \hbox (122.24593pt too wide) in paragraph at lines 915--915 [] \OT1/cmtt/m/n/10 write(*,*)'Please provide the x, y and z parameters that de fine the size of the region:'[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !------------------------------------------------------- ----------------[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1010--1010 [] \OT1/cmtt/m/n/10 Plot_VGB(iPlotVar,i,j,k,iBlock) = State_VGB(Rho_,i,j ,k,iBlock)[] [19] [20] [21] [22] [23] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 Beta ! not specific, beta can be a lot of things[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 nGrid_Points ! difficult to remember, not unique[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 CentripetalForce ! misleading if it is really centrifugal force[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 CristophelCoeff ! pretentious when it simply means face area/dx[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 UseCT ! incomprehensible for non-e xperts[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1127--1127 []\OT1/cmtt/m/n/10 integer:: iMethods ! 1 = Roe scheme, 2 = HLL scheme, 3 = Lax-Friedricsh[] [24] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1127--1127 []\OT1/cmtt/m/n/10 logical:: FirstOrder ! .true. = first order, .false. = s econd order[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1164--1164 []\OT1/cmtt/m/n/10 integer :: nOrder ! 1 = first order, 2 = second order[] [25] Overfull \hbox (11.80951pt too wide) in paragraph at lines 1185--1189 []\OT1/cmr/m/n/10 If a num-ber has to be sin-gle or dou-ble pre-ci-sion, we use the \OT1/cmtt/m/n/10 selected[]real[]kind [26] [27] Overfull \hbox (32.9967pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 Config.pl configuration script (using share/Script s/Config.pl)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 Makefile with targets install, LIB, rundir, clean , distclean[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 output/ reference solutions of the functionality tests[] [28] [29] [30] [31] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 logical:: DoneComputation ! done with the co mputation[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 logical:: UseConstrainedB ! use constrained transport scheme[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 integer:: MaxBlock ! maximum number o f blocks[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 integer:: MinBoundary ! minimum value of boundary index[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 character(len=20):: TypeFlux ! type of the nume rical flux[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 character(len=100):: StringLogVar ! variables saved into the log file[] Overfull \hbox (17.41568pt too wide) in paragraph at lines 1568--1590 [] [32] [33] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 B0x_XB(:,:,:,:) - real array indexed by the X faces and blocks[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 nRoot_D(:) - integer array indexed by the 3 directi ons (x,y,z)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 Buffer_VII(:,:,:) - real buffer with one variable and two other indexes[] [34] [35] (./SOFTWARE_STANDARD.aux) ) (see the transcript file for additional information) Output written on SOFTWARE_STANDARD.pdf (35 pages, 200037 bytes). Transcript written on SOFTWARE_STANDARD.log. makeindex SOFTWARE_STANDARD.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file SOFTWARE_STANDARD.idx...done (0 entries accepted, 0 rejected). Nothing written in SOFTWARE_STANDARD.ind. Transcript written in SOFTWARE_STANDARD.ilg. pdflatex SOFTWARE_STANDARD.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./SOFTWARE_STANDARD.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./SOFTWARE_STANDARD.aux) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/upd map/pdftex.map}] (./SOFTWARE_STANDARD.toc) [2] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] [5] [6] [7] [8] [9] [10] Overfull \hbox (59.24648pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_block_lu ! LU preconditioner for up to hep ta block-diagonal[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_upper ! multiply with upper block trian gular matrix[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 486--486 [] \OT1/cmtt/m/n/10 public:: linear_lower ! multiply with lower block trian gular matrix[] [11] [12] Overfull \hbox (32.9967pt too wide) in paragraph at lines 547--547 [] \OT1/cmtt/m/n/10 public:: sph_to_xyz ! convert spherical into Cartesian coordinates[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 547--547 [] \OT1/cmtt/m/n/10 module procedure sph_to_xyz11, sph_to_xyz13, sph_to_xyz 31, sph_to_xyz33[] [13] [14] Overfull \hbox (6.74693pt too wide) in paragraph at lines 696--696 [] \OT1/cmtt/m/n/10 if(.not. allocated(Matrix_II)) allocate(Matrix_II(nColumn ,nRow))[] [15] Overfull \hbox (1.49698pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 use BALT_lib, ONLY: MinI, MaxI, MinJ, MaxJ, MinK, MaxK, Ma xBlock[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 !========================================================= ===============[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 728--728 [] \OT1/cmtt/m/n/10 allocate(State_VGB(nVar,MinI:MaxI,MinJ:MaxJ,MinK:MaxK,M axBlock))[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 type(StateType):: State_GB(MinI:MaxI,MinJ:MaxJ,MinK:MaxK,M axBlock)[] [16] [17] Overfull \hbox (22.4968pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Velocity0 ! the shear velocity far from the s hear layer[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Width ! the width of the layer in the Y d irection[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 815--815 [] \OT1/cmtt/m/n/10 real:: Perturbation ! the perturbation in the Y compone nt of velocity[] [18] Overfull \hbox (122.24593pt too wide) in paragraph at lines 915--915 [] \OT1/cmtt/m/n/10 write(*,*)'Please provide the x, y and z parameters that de fine the size of the region:'[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !------------------------------------------------------- ----------------[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 969--969 [] \OT1/cmtt/m/n/10 !========================================================= ================[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1010--1010 [] \OT1/cmtt/m/n/10 Plot_VGB(iPlotVar,i,j,k,iBlock) = State_VGB(Rho_,i,j ,k,iBlock)[] [19] [20] [21] [22] [23] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 Beta ! not specific, beta can be a lot of things[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 nGrid_Points ! difficult to remember, not unique[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 CentripetalForce ! misleading if it is really centrifugal force[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 CristophelCoeff ! pretentious when it simply means face area/dx[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1089--1089 []\OT1/cmtt/m/n/10 UseCT ! incomprehensible for non-e xperts[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1127--1127 []\OT1/cmtt/m/n/10 integer:: iMethods ! 1 = Roe scheme, 2 = HLL scheme, 3 = Lax-Friedricsh[] [24] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1127--1127 []\OT1/cmtt/m/n/10 logical:: FirstOrder ! .true. = first order, .false. = s econd order[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1164--1164 []\OT1/cmtt/m/n/10 integer :: nOrder ! 1 = first order, 2 = second order[] [25] Overfull \hbox (11.80951pt too wide) in paragraph at lines 1185--1189 []\OT1/cmr/m/n/10 If a num-ber has to be sin-gle or dou-ble pre-ci-sion, we use the \OT1/cmtt/m/n/10 selected[]real[]kind [26] [27] Overfull \hbox (32.9967pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 Config.pl configuration script (using share/Script s/Config.pl)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 Makefile with targets install, LIB, rundir, clean , distclean[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1343--1343 []\OT1/cmtt/m/n/10 output/ reference solutions of the functionality tests[] [28] [29] [30] [31] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 logical:: DoneComputation ! done with the co mputation[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 logical:: UseConstrainedB ! use constrained transport scheme[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 integer:: MaxBlock ! maximum number o f blocks[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 integer:: MinBoundary ! minimum value of boundary index[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 character(len=20):: TypeFlux ! type of the nume rical flux[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1561--1561 []\OT1/cmtt/m/n/10 character(len=100):: StringLogVar ! variables saved into the log file[] Overfull \hbox (17.41568pt too wide) in paragraph at lines 1568--1590 [] [32] [33] Overfull \hbox (1.49698pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 B0x_XB(:,:,:,:) - real array indexed by the X faces and blocks[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 nRoot_D(:) - integer array indexed by the 3 directi ons (x,y,z)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1608--1608 [] \OT1/cmtt/m/n/10 Buffer_VII(:,:,:) - real buffer with one variable and two other indexes[] [34] [35] (./SOFTWARE_STANDARD.aux) ) (see the transcript file for additional information) Output written on SOFTWARE_STANDARD.pdf (35 pages, 200037 bytes). Transcript written on SOFTWARE_STANDARD.log. mv SOFTWARE_STANDARD.pdf ../ rm -f SOFTWARE_STANDARD.ind SOFTWARE_STANDARD.idx SOFTWARE_STANDARD.ilg make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/doc/Tex' make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/CRASH/doc/Tex' touch ionization_equilibrium.ind ionization_equilibrium.idx pdflatex ionization_equilibrium.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ionization_equilibrium.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) LaTeX Warning: Unused global option(s): [english]. No file ionization_equilibrium.aux. LaTeX Warning: No \author given. Overfull \hbox (19.32724pt too wide) in paragraph at lines 26--31 \OT1/cmr/m/n/12 doci-ment. The For-tran code will au-to-mat-i-cally com-pile th e ex-e-cutable IONIZ.exe [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] [8] [9] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [10] (./ionization_table1.tex) [11] [12] LaTeX Warning: Reference `sec:Temperature-Calculation' on page 13 undefined on input line 449. [13] LaTeX Warning: Reference `eq:26' on page 14 undefined on input line 489. LaTeX Warning: Reference `eq:26' on page 14 undefined on input line 492. LaTeX Warning: Reference `eq:6' on page 14 undefined on input line 498. Overfull \hbox (104.1642pt too wide) in alignment at lines 510--513 [][][] [] [14] LaTeX Warning: Reference `eq:32' on page 15 undefined on input line 520. LaTeX Warning: Reference `eq:33' on page 15 undefined on input line 526. Overfull \hbox (107.5706pt too wide) in alignment at lines 527--532 [][][] [] Overfull \hbox (26.70114pt too wide) detected at line 542 [] \OML/cmm/m/it/12 < \OT1/cmr/m/n/12 (\OML/cmm/m/it/12 a\OMS/cmsy/m/n/12 ^^ @ \OML/cmm/m/it/12 < a >\OT1/cmr/m/n/12 ) (\OML/cmm/m/it/12 b\OMS/cmsy/m/n/12 ^ ^@ \OML/cmm/m/it/12 < b >\OT1/cmr/m/n/12 ) \OML/cmm/m/it/12 >\OT1/cmr/m/n/12 =\ OML/cmm/m/it/12 < ab \OMS/cmsy/m/n/12 ^^@ \OML/cmm/m/it/12 a < b > \OMS/cmsy/m/ n/12 ^^@\OML/cmm/m/it/12 b < a > \OT1/cmr/m/n/12 + \OML/cmm/m/it/12 < a >< b >> \OT1/cmr/m/n/12 = LaTeX Warning: Reference `eq:20' on page 15 undefined on input line 549. LaTeX Warning: Reference `eq:35' on page 15 undefined on input line 550. LaTeX Warning: Reference `eq:32' on page 15 undefined on input line 550. Overfull \hbox (26.69366pt too wide) in alignment at lines 551--554 [][][] [] [15] LaTeX Warning: Reference `eq:31' on page 16 undefined on input line 556. Overfull \hbox (43.54182pt too wide) in alignment at lines 557--560 [][][] [] LaTeX Warning: Reference `eq:29' on page 16 undefined on input line 562. LaTeX Warning: Reference `eq:36' on page 16 undefined on input line 563. LaTeX Warning: Reference `eq:38' on page 16 undefined on input line 568. LaTeX Warning: Reference `eq:29' on page 16 undefined on input line 568. Overfull \hbox (142.71425pt too wide) in alignment at lines 570--581 [][][] [] LaTeX Warning: Reference `eq:26' on page 16 undefined on input line 584. [16] (./ionization_table2.tex) Overfull \hbox (234.70699pt too wide) in paragraph at lines 3--592 [] LaTeX Warning: Reference `eq:26' on page 17 undefined on input line 602. [17] Overfull \hbox (13.68956pt too wide) detected at line 619 \OML/cmm/m/it/12 C[] \OT1/cmr/m/n/12 = [](1 + \OML/cmm/m/it/12 Z\OT1/cmr/m/n/12 )+ \OML/cmm/m/it/12 < [][] > \OT1/cmr/m/n/12 +[]\OML/cmm/m/it/12 ; LaTeX Warning: Reference `sec:Ionization-Equilibrium' on page 18 undefined on i nput line 622. [18] (./ionization_table3.tex) Overfull \hbox (199.82402pt too wide) in paragraph at lines 3--650 [] [19] Overfull \vbox (73.6991pt too high) has occurred while \output is active [20] (./ionization_table4.tex) Overfull \hbox (199.82402pt too wide) in paragraph at lines 3--656 [] [21] Overfull \vbox (73.6991pt too high) has occurred while \output is active [22] LaTeX Warning: Reference `eq:Cj' on page 23 undefined on input line 686. LaTeX Warning: Reference `eq:Pij' on page 23 undefined on input line 686. LaTeX Warning: Reference `eq:3' on page 23 undefined on input line 696. [23] LaTeX Warning: Reference `eq:6' on page 24 undefined on input line 715. LaTeX Warning: Reference `eq:Saha' on page 24 undefined on input line 715. LaTeX Warning: Reference `eq:13' on page 24 undefined on input line 719. LaTeX Warning: Reference `eq:Zmix' on page 24 undefined on input line 720. LaTeX Warning: Reference `eq:18' on page 24 undefined on input line 729. [24] Overfull \hbox (0.32893pt too wide) in paragraph at lines 738--743 \OT1/cmr/m/n/12 Here, once again, for any ex-pres-sion $\OML/cmm/m/it/12 a; < a >[]\OT1/cmr/m/n/12 = []$. LaTeX Warning: Reference `eq:26' on page 25 undefined on input line 745. LaTeX Warning: Reference `eq:Umix' on page 25 undefined on input line 756. LaTeX Warning: Reference `eq:41' on page 25 undefined on input line 756. LaTeX Warning: Reference `eq:35' on page 25 undefined on input line 756. [25] LaTeX Warning: Reference `eq:Cv' on page 26 undefined on input line 762. LaTeX Warning: Reference `eq:Umix' on page 26 undefined on input line 762. Overfull \hbox (148.79991pt too wide) in alignment at lines 763--766 [][][] [] Overfull \hbox (36.57945pt too wide) detected at line 770 \OML/cmm/m/it/12 C[] \OT1/cmr/m/n/12 = [](1 + \OML/cmm/m/it/12 Z\OT1/cmr/m/n/12 )+ \OMS/cmsy/m/n/12 ^^\ [][] ^^] \OT1/cmr/m/n/12 +[]\OML/cmm/m/it/12 ;[] Overfull \hbox (76.40097pt too wide) in paragraph at lines 770--772 \OT1/cmr/m/n/12 where for any ex-pres-sions $\OML/cmm/m/it/12 a$ \OT1/cmr/m/n/1 2 and $\OML/cmm/m/it/12 b; \OMS/cmsy/m/n/12 ^^\ \OML/cmm/m/it/12 ^^Na ^^Nb \OMS /cmsy/m/n/12 ^^]\OT1/cmr/m/n/12 = [][] []$. LaTeX Warning: Reference `eq:CalcT' on page 26 undefined on input line 776. (./ionization_table5.tex) Overfull \hbox (187.70747pt too wide) in paragraph at lines 3--781 [] [26] [27] [28] (./ionization_equilibrium.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on ionization_equilibrium.pdf (28 pages, 217063 bytes). Transcript written on ionization_equilibrium.log. makeindex ionization_equilibrium.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file ionization_equilibrium.idx...done (0 entries accepted, 0 rejected). Nothing written in ionization_equilibrium.ind. Transcript written in ionization_equilibrium.ilg. pdflatex ionization_equilibrium.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ionization_equilibrium.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) LaTeX Warning: Unused global option(s): [english]. (./ionization_equilibrium.aux) LaTeX Warning: No \author given. Overfull \hbox (19.32724pt too wide) in paragraph at lines 26--31 \OT1/cmr/m/n/12 doci-ment. The For-tran code will au-to-mat-i-cally com-pile th e ex-e-cutable IONIZ.exe [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] [8] [9] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [10] (./ionization_table1.tex) [11] [12] [13] Overfull \hbox (104.1642pt too wide) in alignment at lines 510--513 [][][] [] [14] Overfull \hbox (107.5706pt too wide) in alignment at lines 527--532 [][][] [] Overfull \hbox (26.70114pt too wide) detected at line 542 [] \OML/cmm/m/it/12 < \OT1/cmr/m/n/12 (\OML/cmm/m/it/12 a\OMS/cmsy/m/n/12 ^^ @ \OML/cmm/m/it/12 < a >\OT1/cmr/m/n/12 ) (\OML/cmm/m/it/12 b\OMS/cmsy/m/n/12 ^ ^@ \OML/cmm/m/it/12 < b >\OT1/cmr/m/n/12 ) \OML/cmm/m/it/12 >\OT1/cmr/m/n/12 =\ OML/cmm/m/it/12 < ab \OMS/cmsy/m/n/12 ^^@ \OML/cmm/m/it/12 a < b > \OMS/cmsy/m/ n/12 ^^@\OML/cmm/m/it/12 b < a > \OT1/cmr/m/n/12 + \OML/cmm/m/it/12 < a >< b >> \OT1/cmr/m/n/12 = Overfull \hbox (26.69366pt too wide) in alignment at lines 551--554 [][][] [] [15] Overfull \hbox (43.54182pt too wide) in alignment at lines 557--560 [][][] [] Overfull \hbox (142.71425pt too wide) in alignment at lines 570--581 [][][] [] [16] (./ionization_table2.tex) Overfull \hbox (234.70699pt too wide) in paragraph at lines 3--592 [] [17] Overfull \hbox (13.68956pt too wide) detected at line 619 \OML/cmm/m/it/12 C[] \OT1/cmr/m/n/12 = [](1 + \OML/cmm/m/it/12 Z\OT1/cmr/m/n/12 )+ \OML/cmm/m/it/12 < [][] > \OT1/cmr/m/n/12 +[]\OML/cmm/m/it/12 ; [18] (./ionization_table3.tex) Overfull \hbox (199.82402pt too wide) in paragraph at lines 3--650 [] [19] Overfull \vbox (73.6991pt too high) has occurred while \output is active [20] (./ionization_table4.tex) Overfull \hbox (199.82402pt too wide) in paragraph at lines 3--656 [] [21] Overfull \vbox (73.6991pt too high) has occurred while \output is active [22] [23] [24] Overfull \hbox (0.32893pt too wide) in paragraph at lines 738--743 \OT1/cmr/m/n/12 Here, once again, for any ex-pres-sion $\OML/cmm/m/it/12 a; < a >[]\OT1/cmr/m/n/12 = []$. [25] Overfull \hbox (148.79991pt too wide) in alignment at lines 763--766 [][][] [] Overfull \hbox (36.57945pt too wide) detected at line 770 \OML/cmm/m/it/12 C[] \OT1/cmr/m/n/12 = [](1 + \OML/cmm/m/it/12 Z\OT1/cmr/m/n/12 )+ \OMS/cmsy/m/n/12 ^^\ [][] ^^] \OT1/cmr/m/n/12 +[]\OML/cmm/m/it/12 ;[] Overfull \hbox (76.40097pt too wide) in paragraph at lines 770--772 \OT1/cmr/m/n/12 where for any ex-pres-sions $\OML/cmm/m/it/12 a$ \OT1/cmr/m/n/1 2 and $\OML/cmm/m/it/12 b; \OMS/cmsy/m/n/12 ^^\ \OML/cmm/m/it/12 ^^Na ^^Nb \OMS /cmsy/m/n/12 ^^]\OT1/cmr/m/n/12 = [][] []$. (./ionization_table5.tex) Overfull \hbox (187.70747pt too wide) in paragraph at lines 3--781 [] [26] [27] [28] (./ionization_equilibrium.aux) ) (see the transcript file for additional information) Output written on ionization_equilibrium.pdf (28 pages, 216480 bytes). Transcript written on ionization_equilibrium.log. makeindex ionization_equilibrium.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file ionization_equilibrium.idx...done (0 entries accepted, 0 rejected). Nothing written in ionization_equilibrium.ind. Transcript written in ionization_equilibrium.ilg. pdflatex ionization_equilibrium.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ionization_equilibrium.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) LaTeX Warning: Unused global option(s): [english]. (./ionization_equilibrium.aux) LaTeX Warning: No \author given. Overfull \hbox (19.32724pt too wide) in paragraph at lines 26--31 \OT1/cmr/m/n/12 doci-ment. The For-tran code will au-to-mat-i-cally com-pile th e ex-e-cutable IONIZ.exe [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] [8] [9] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [10] (./ionization_table1.tex) [11] [12] [13] Overfull \hbox (104.1642pt too wide) in alignment at lines 510--513 [][][] [] [14] Overfull \hbox (107.5706pt too wide) in alignment at lines 527--532 [][][] [] Overfull \hbox (26.70114pt too wide) detected at line 542 [] \OML/cmm/m/it/12 < \OT1/cmr/m/n/12 (\OML/cmm/m/it/12 a\OMS/cmsy/m/n/12 ^^ @ \OML/cmm/m/it/12 < a >\OT1/cmr/m/n/12 ) (\OML/cmm/m/it/12 b\OMS/cmsy/m/n/12 ^ ^@ \OML/cmm/m/it/12 < b >\OT1/cmr/m/n/12 ) \OML/cmm/m/it/12 >\OT1/cmr/m/n/12 =\ OML/cmm/m/it/12 < ab \OMS/cmsy/m/n/12 ^^@ \OML/cmm/m/it/12 a < b > \OMS/cmsy/m/ n/12 ^^@\OML/cmm/m/it/12 b < a > \OT1/cmr/m/n/12 + \OML/cmm/m/it/12 < a >< b >> \OT1/cmr/m/n/12 = Overfull \hbox (26.69366pt too wide) in alignment at lines 551--554 [][][] [] [15] Overfull \hbox (43.54182pt too wide) in alignment at lines 557--560 [][][] [] Overfull \hbox (142.71425pt too wide) in alignment at lines 570--581 [][][] [] [16] (./ionization_table2.tex) Overfull \hbox (234.70699pt too wide) in paragraph at lines 3--592 [] [17] Overfull \hbox (13.68956pt too wide) detected at line 619 \OML/cmm/m/it/12 C[] \OT1/cmr/m/n/12 = [](1 + \OML/cmm/m/it/12 Z\OT1/cmr/m/n/12 )+ \OML/cmm/m/it/12 < [][] > \OT1/cmr/m/n/12 +[]\OML/cmm/m/it/12 ; [18] (./ionization_table3.tex) Overfull \hbox (199.82402pt too wide) in paragraph at lines 3--650 [] [19] Overfull \vbox (73.6991pt too high) has occurred while \output is active [20] (./ionization_table4.tex) Overfull \hbox (199.82402pt too wide) in paragraph at lines 3--656 [] [21] Overfull \vbox (73.6991pt too high) has occurred while \output is active [22] [23] [24] Overfull \hbox (0.32893pt too wide) in paragraph at lines 738--743 \OT1/cmr/m/n/12 Here, once again, for any ex-pres-sion $\OML/cmm/m/it/12 a; < a >[]\OT1/cmr/m/n/12 = []$. [25] Overfull \hbox (148.79991pt too wide) in alignment at lines 763--766 [][][] [] Overfull \hbox (36.57945pt too wide) detected at line 770 \OML/cmm/m/it/12 C[] \OT1/cmr/m/n/12 = [](1 + \OML/cmm/m/it/12 Z\OT1/cmr/m/n/12 )+ \OMS/cmsy/m/n/12 ^^\ [][] ^^] \OT1/cmr/m/n/12 +[]\OML/cmm/m/it/12 ;[] Overfull \hbox (76.40097pt too wide) in paragraph at lines 770--772 \OT1/cmr/m/n/12 where for any ex-pres-sions $\OML/cmm/m/it/12 a$ \OT1/cmr/m/n/1 2 and $\OML/cmm/m/it/12 b; \OMS/cmsy/m/n/12 ^^\ \OML/cmm/m/it/12 ^^Na ^^Nb \OMS /cmsy/m/n/12 ^^]\OT1/cmr/m/n/12 = [][] []$. (./ionization_table5.tex) Overfull \hbox (187.70747pt too wide) in paragraph at lines 3--781 [] [26] [27] [28] (./ionization_equilibrium.aux) ) (see the transcript file for additional information) Output written on ionization_equilibrium.pdf (28 pages, 216480 bytes). Transcript written on ionization_equilibrium.log. mv ionization_equilibrium.pdf ../ rm -f ionization_equilibrium.ind ionization_equilibrium.idx ionization_equilibrium.ilg touch EvidenceFile.ind EvidenceFile.idx pdflatex EvidenceFile.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./EvidenceFile.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) No file EvidenceFile.aux. LaTeX Warning: No \author given. [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] Overfull \vbox (87.79115pt too high) has occurred while \output is active [2] (./EvidenceFile.aux) ) (see the transcript file for additional information) Output written on EvidenceFile.pdf (2 pages, 51758 bytes). Transcript written on EvidenceFile.log. makeindex EvidenceFile.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file EvidenceFile.idx...done (0 entries accepted, 0 rejected). Nothing written in EvidenceFile.ind. Transcript written in EvidenceFile.ilg. pdflatex EvidenceFile.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./EvidenceFile.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./EvidenceFile.aux) LaTeX Warning: No \author given. [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] Overfull \vbox (87.79115pt too high) has occurred while \output is active [2] (./EvidenceFile.aux) ) (see the transcript file for additional information) Output written on EvidenceFile.pdf (2 pages, 51758 bytes). Transcript written on EvidenceFile.log. makeindex EvidenceFile.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file EvidenceFile.idx...done (0 entries accepted, 0 rejected). Nothing written in EvidenceFile.ind. Transcript written in EvidenceFile.ilg. pdflatex EvidenceFile.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./EvidenceFile.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./EvidenceFile.aux) LaTeX Warning: No \author given. [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] Overfull \vbox (87.79115pt too high) has occurred while \output is active [2] (./EvidenceFile.aux) ) (see the transcript file for additional information) Output written on EvidenceFile.pdf (2 pages, 51758 bytes). Transcript written on EvidenceFile.log. mv EvidenceFile.pdf ../ rm -f EvidenceFile.ind EvidenceFile.idx EvidenceFile.ilg touch GrayDiffusion.ind GrayDiffusion.idx pdflatex GrayDiffusion.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./GrayDiffusion.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) No file GrayDiffusion.aux. LaTeX Warning: Reference `eq:density' on page 1 undefined on input line 45. LaTeX Warning: Reference `eq:gray' on page 1 undefined on input line 45. [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] LaTeX Warning: Reference `eq:density' on page 2 undefined on input line 71. LaTeX Warning: Reference `eq:gray' on page 2 undefined on input line 71. LaTeX Warning: Reference `eq:gray' on page 2 undefined on input line 84. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [2] LaTeX Warning: Reference `eq:hydro1' on page 3 undefined on input line 108. LaTeX Warning: Reference `eq:hydro2' on page 3 undefined on input line 108. LaTeX Warning: Reference `eq:hydro3' on page 3 undefined on input line 108. LaTeX Warning: Reference `eq:deficit1' on page 3 undefined on input line 110. LaTeX Warning: Reference `eq:deficit2' on page 3 undefined on input line 110. LaTeX Warning: Reference `eq:deficit1' on page 3 undefined on input line 122. LaTeX Warning: Reference `eq:deficit2' on page 3 undefined on input line 122. LaTeX Warning: Reference `eq:eint' on page 3 undefined on input line 144. LaTeX Warning: Reference `eq:erad' on page 3 undefined on input line 144. [3] LaTeX Warning: Reference `eq:Eint2' on page 4 undefined on input line 164. LaTeX Warning: Reference `eq:Erad2' on page 4 undefined on input line 165. LaTeX Warning: Reference `eq:Eint2' on page 4 undefined on input line 166. LaTeX Warning: Reference `eq:Erad2' on page 4 undefined on input line 167. LaTeX Warning: Reference `eq:Erad2' on page 4 undefined on input line 168. LaTeX Warning: Reference `eq:Eint2' on page 4 undefined on input line 174. LaTeX Warning: Reference `eq:Eint2' on page 4 undefined on input line 186. LaTeX Warning: Reference `eq:B' on page 4 undefined on input line 195. LaTeX Warning: Reference `eq:Erad2' on page 4 undefined on input line 200. [4] LaTeX Warning: Reference `eq:Erad3' on page 5 undefined on input line 217. LaTeX Warning: Reference `eq:DeltaErad' on page 5 undefined on input line 224. LaTeX Warning: Reference `eq:B2' on page 5 undefined on input line 228. [5] LaTeX Warning: Reference `eq:B4' on page 6 undefined on input line 257. LaTeX Warning: Reference `eq:Erad4' on page 6 undefined on input line 264. Overfull \hbox (13.12914pt too wide) in alignment at lines 265--273 [][][] [] LaTeX Warning: Reference `eq:Erad5' on page 6 undefined on input line 287. LaTeX Warning: Reference `eq:DeltaErad2' on page 6 undefined on input line 296. LaTeX Warning: Reference `eq:K5' on page 6 undefined on input line 296. LaTeX Warning: Reference `eq:DeltaErad2' on page 6 undefined on input line 298. LaTeX Warning: Reference `eq:B5' on page 6 undefined on input line 300. [6] [7] (./GrayDiffusion.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on GrayDiffusion.pdf (7 pages, 106069 bytes). Transcript written on GrayDiffusion.log. makeindex GrayDiffusion.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file GrayDiffusion.idx...done (0 entries accepted, 0 rejected). Nothing written in GrayDiffusion.ind. Transcript written in GrayDiffusion.ilg. pdflatex GrayDiffusion.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./GrayDiffusion.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (./GrayDiffusion.aux ) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [2] [3] [4] [5] Overfull \hbox (13.12914pt too wide) in alignment at lines 265--273 [][][] [] [6] [7] (./GrayDiffusion.aux) ) (see the transcript file for additional information) Output written on GrayDiffusion.pdf (7 pages, 105533 bytes). Transcript written on GrayDiffusion.log. makeindex GrayDiffusion.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file GrayDiffusion.idx...done (0 entries accepted, 0 rejected). Nothing written in GrayDiffusion.ind. Transcript written in GrayDiffusion.ilg. pdflatex GrayDiffusion.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./GrayDiffusion.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (./GrayDiffusion.aux ) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [2] [3] [4] [5] Overfull \hbox (13.12914pt too wide) in alignment at lines 265--273 [][][] [] [6] [7] (./GrayDiffusion.aux) ) (see the transcript file for additional information) Output written on GrayDiffusion.pdf (7 pages, 105533 bytes). Transcript written on GrayDiffusion.log. mv GrayDiffusion.pdf ../ rm -f GrayDiffusion.ind GrayDiffusion.idx GrayDiffusion.ilg touch HEDP.ind HEDP.idx pdflatex HEDP.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./HEDP.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) LaTeX Warning: Unused global option(s): [english]. No file HEDP.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) LaTeX Warning: No \author given. LaTeX Warning: Citation `ZR' on page 1 undefined on input line 34. LaTeX Warning: Citation `ll' on page 1 undefined on input line 50. [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./HEDP_Part1.tex (./FermiStatistics.tex LaTeX Warning: Citation `ll' on page 3 undefined on input line 20. LaTeX Warning: Citation `ll' on page 3 undefined on input line 27. [3] LaTeX Warning: Reference `saharecursive' on page 4 undefined on input line 65. [4] LaTeX Warning: Citation `ll' on page 5 undefined on input line 96. LaTeX Warning: Reference `zavr' on page 5 undefined on input line 100. LaTeX Warning: Reference `zfe' on page 5 undefined on input line 100. [5] LaTeX Warning: Reference `zavr' on page 6 undefined on input line 134. LaTeX Warning: Reference `zfe' on page 6 undefined on input line 134. LaTeX Warning: Reference `iter' on page 6 undefined on input line 143. LaTeX Warning: Reference `differmean' on page 6 undefined on input line 151. LaTeX Warning: Reference `iter' on page 6 undefined on input line 153. LaTeX Warning: Reference `feboltzmann' on page 6 undefined on input line 156. LaTeX Warning: Reference `iter' on page 6 undefined on input line 156. LaTeX Warning: Reference `iter' on page 6 undefined on input line 159. LaTeX Warning: Reference `iter' on page 6 undefined on input line 161. [6] LaTeX Warning: Reference `freeenergy' on page 7 undefined on input line 169. LaTeX Warning: Citation `ll' on page 7 undefined on input line 173. LaTeX Warning: Reference `equile' on page 7 undefined on input line 177. LaTeX Warning: Reference `equile' on page 7 undefined on input line 184. Overfull \hbox (32.89856pt too wide) detected at line 192 \OMS/cmsy/m/n/12 E \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 ^^@[] [] \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 + \OMS/cmsy/m/n/12 E[]\OML/cmm/m/it/12 ; \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 = []\OML/cmm/m/it/12 Tn[]; \OMS/cmsy/m/ n/12 E[] \OT1/cmr/m/n/12 = \OML/cmm/m/it/12 n[] [] ; [7] LaTeX Warning: Citation `drake' on page 8 undefined on input line 229. LaTeX Warning: Citation `drake' on page 8 undefined on input line 235. [8] LaTeX Warning: Reference `diffge' on page 9 undefined on input line 250. LaTeX Warning: Reference `diffz' on page 9 undefined on input line 250. LaTeX Warning: Reference `feboltzmann' on page 9 undefined on input line 251. LaTeX Warning: Reference `diffge' on page 9 undefined on input line 260. LaTeX Warning: Reference `diffz' on page 9 undefined on input line 260. LaTeX Warning: Reference `diffge' on page 9 undefined on input line 261. LaTeX Warning: Reference `diffz' on page 9 undefined on input line 261. Overfull \hbox (0.18669pt too wide) in paragraph at lines 260--262 []\OT1/cmr/m/n/12 Assuming $\OML/cmm/m/it/12 ^^N[]$ \OT1/cmr/m/n/12 to be a sma ll in-cre-ment in the right hand side of Eqs.([],[]), ) (./Coulomb.tex Overfull \hbox (8.76778pt too wide) in paragraph at lines 3--3 []\OT1/cmr/bx/n/17.28 Madelung ap-prox-i-ma-tion of elec-tro-static en- [9] LaTeX Warning: Citation `drake' on page 10 undefined on input line 26. [10] LaTeX Warning: Reference `pfM' on page 11 undefined on input line 62. [11] LaTeX Warning: Reference `iter' on page 12 undefined on input line 98. LaTeX Warning: Reference `fterm' on page 12 undefined on input line 100. LaTeX Warning: Reference `ni' on page 12 undefined on input line 109. LaTeX Warning: Reference `fe1' on page 12 undefined on input line 109. LaTeX Warning: Reference `ffullm' on page 12 undefined on input line 116. Overfull \hbox (15.74991pt too wide) detected at line 127 []\OMS/cmsy/m/n/12 E \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 ^^@[] [] \OT1/cmr/m/n/1 2 = \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 + \OMS/cmsy/m/n/12 E[]\OML/cmm/m/it/12 ; \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 = []\OML/cmm/m/it/12 Tn[]; \OMS/cmsy/ m/n/12 E[] \OT1/cmr/m/n/12 = \OML/cmm/m/it/12 n[] [] ; [12] LaTeX Warning: Reference `estar' on page 13 undefined on input line 133. LaTeX Warning: Reference `estar' on page 13 undefined on input line 172. LaTeX Warning: Reference `estar' on page 13 undefined on input line 178. LaTeX Warning: Reference `estarprime' on page 13 undefined on input line 178. [13] (./ionization_table7.tex) Overfull \hbox (85.39262pt too wide) in paragraph at lines 3--191 [] [14]) (./Excitation.tex LaTeX Warning: Citation `spectrw3' on page 15 undefined on input line 39. LaTeX Warning: Citation `nistdb' on page 15 undefined on input line 39. LaTeX Warning: Citation `RefAlMartin' on page 15 undefined on input line 39. LaTeX Warning: Citation `RefXeSaloman' on page 15 undefined on input line 39. LaTeX Warning: Citation `Carlson' on page 15 undefined on input line 46. LaTeX Warning: Citation `allenAQ' on page 15 undefined on input line 47. LaTeX Warning: Reference `generalE' on page 15 undefined on input line 56. LaTeX Warning: Reference `generalP' on page 15 undefined on input line 56. LaTeX Warning: Reference `generalCv' on page 15 undefined on input line 56. LaTeX Warning: Reference `generalPT' on page 15 undefined on input line 57. LaTeX Warning: Reference `generalCompr' on page 15 undefined on input line 57. LaTeX Warning: Reference `estarin' on page 15 undefined on input line 57. [15] LaTeX Warning: Reference `sepcov' on page 16 undefined on input line 60. LaTeX Warning: Reference `estarin' on page 16 undefined on input line 63. ) (./PressureIonization.tex LaTeX Warning: Reference `generalE' on page 16 undefined on input line 25. LaTeX Warning: Reference `generalP' on page 16 undefined on input line 25. LaTeX Warning: Reference `generalCv' on page 16 undefined on input line 25. LaTeX Warning: Reference `generalPT' on page 16 undefined on input line 26. LaTeX Warning: Reference `generalCompr' on page 16 undefined on input line 26. [16] LaTeX Warning: Reference `sepcov' on page 17 undefined on input line 68. Overfull \hbox (32.54692pt too wide) detected at line 107 \OMS/cmsy/m/n/12 ^^@[]h\OML/cmm/m/it/12 ^^N[]^^NE\OMS/cmsy/m/n/12 i \OT1/cmr/m/ n/12 = \OMS/cmsy/m/n/12 ^^@[]h\OML/cmm/m/it/12 ^^N[]^^N\OMS/cmsy/m/n/12 h\OML/c mm/m/it/12 E\OMS/cmsy/m/n/12 i[]i[] ^^@ []hh\OML/cmm/m/it/12 ^^NE[]^^N[]\OMS/cm sy/m/n/12 i[]i[] ^^@ []h\OML/cmm/m/it/12 ^^N\OMS/cmsy/m/n/12 h[]i[]\OML/cmm/m/i t/12 ^^N\OMS/cmsy/m/n/12 h\OML/cmm/m/it/12 E\OMS/cmsy/m/n/12 i[]i[]\OML/cmm/m/i t/12 : )) [17] (./HEDP_Part2.tex (./MultiGroup.tex Overfull \hbox (50.42183pt too wide) detected at line 38 [][] \OT1/cmr/m/n/14.4 + \OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/m/n/14.4 ([]\OML/cmm /m/it/14.4 E[]\OT1/cmr/m/n/14.4 ) \OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 (\OM L/cmm/m/it/14.4 ^^M[] \OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 1)(\OMS/cmsy/m/n /14.4 r ^^A \OT1/cmr/bx/n/14.4 u\OT1/cmr/m/n/14.4 )\OML/cmm/m/it/14.4 "[] \OT1/ cmr/m/n/14.4 = []\OML/cmm/m/it/14.4 : LaTeX Warning: Reference `eq:mg1' on page 18 undefined on input line 39. LaTeX Warning: Reference `eq:mg1' on page 18 undefined on input line 42. [18] LaTeX Warning: Reference `eq:mg0' on page 19 undefined on input line 51. LaTeX Warning: Reference `eq:mg2' on page 19 undefined on input line 51. LaTeX Warning: Reference `eq:mg1' on page 19 undefined on input line 69. Overfull \hbox (21.41643pt too wide) in alignment at lines 70--85 [][][] [] LaTeX Warning: Reference `eq:mg4' on page 19 undefined on input line 86. LaTeX Warning: Reference `eq:mg5' on page 19 undefined on input line 86. [19] Overfull \hbox (108.69894pt too wide) in alignment at lines 88--102 [][][] [] LaTeX Warning: Reference `eq:mg6' on page 20 undefined on input line 109. [20] LaTeX Warning: Reference `eq:mg6' on page 21 undefined on input line 121. LaTeX Warning: Reference `eq:mg7' on page 21 undefined on input line 121. LaTeX Warning: Reference `eq:mg6' on page 21 undefined on input line 125. Overfull \hbox (67.79787pt too wide) detected at line 130 [][] \OT1/cmr/m/n/14.4 + \OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/m/n/14.4 (\OT1/cmr/b x/n/14.4 u\OML/cmm/m/it/14.4 E\OT1/cmr/m/n/14.4 ) + (\OML/cmm/m/it/14.4 ^^M[] \ OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 1)(\OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/bx /n/14.4 u\OT1/cmr/m/n/14.4 )\OML/cmm/m/it/14.4 E \OT1/cmr/m/n/14.4 = [][] []\OM L/cmm/m/it/14.4 : LaTeX Warning: Reference `eq:mg8' on page 21 undefined on input line 131. LaTeX Warning: Reference `eq:mg8' on page 21 undefined on input line 131. LaTeX Warning: Reference `eq:mg6' on page 21 undefined on input line 136. [21] Overfull \hbox (113.17989pt too wide) in alignment at lines 141--144 [][][] [] LaTeX Warning: Citation `ZR' on page 22 undefined on input line 155. [22] LaTeX Warning: Reference `eq:mg2' on page 23 undefined on input line 176. LaTeX Warning: Citation `lp' on page 23 undefined on input line 181. [23] LaTeX Warning: Reference `eq:mg2' on page 24 undefined on input line 188. [24] LaTeX Warning: Reference `eq:mg10' on page 25 undefined on input line 218. Overfull \hbox (94.64406pt too wide) detected at line 221 []\OML/cmm/m/it/14.4 N[] \OMS/cmsy/m/n/14.4 / \OML/cmm/m/it/14.4 g[] []\OT1/cmr /m/n/14.4 [\OMS/cmsy/m/n/14.4 ^^@\OML/cmm/m/it/14.4 E[]=\OT1/cmr/m/n/14.4 (\OML /cmm/m/it/14.4 k[]T\OT1/cmr/m/n/14.4 )]\OML/cmm/m/it/14.4 ; [] \OT1/cmr/m/n/14 .4 = [] [] = [][\OMS/cmsy/m/n/14.4 ^^@\OML/cmm/m/it/14.4 "=\OT1/cmr/m/n/14.4 (\ OML/cmm/m/it/14.4 k[]T\OT1/cmr/m/n/14.4 )] Overfull \hbox (5.53162pt too wide) in paragraph at lines 226--228 \OT1/cmr/m/n/14.4 where the ef-fec-tive ab-sorp-tion co-ef-fi-cient, $\OML/cmm/ m/it/14.4 a[]$\OT1/cmr/m/n/14.4 , is in-dro-duced, which LaTeX Warning: Citation `ZR' on page 25 undefined on input line 231. [25] Overfull \hbox (28.41185pt too wide) detected at line 243 []\OML/cmm/m/it/14.4 E[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T; "\OT1/cmr/m/n/ 14.4 ) = \OML/cmm/m/it/14.4 T[][][][]; \OT1/cmr/m/n/14.4 = []\OML/cmm/m/it/ 14.4 ; x \OT1/cmr/m/n/14.4 = []\OML/cmm/m/it/14.4 : LaTeX Warning: Reference `eq:mg12' on page 26 undefined on input line 244. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) LaTeX Warning: Citation `ll' on page 26 undefined on input line 248. ) (./PhotoIonization.tex [26] LaTeX Warning: Citation `ZR' on page 27 undefined on input line 14. LaTeX Warning: Reference `eq:fine' on page 27 undefined on input line 22. LaTeX Warning: Reference `eq:a0' on page 27 undefined on input line 22. LaTeX Warning: Reference `eq:ion' on page 27 undefined on input line 41. [27] LaTeX Warning: Reference `eq:ion' on page 28 undefined on input line 45. LaTeX Warning: Citation `lp' on page 28 undefined on input line 47. LaTeX Warning: Reference `eq:free' on page 28 undefined on input line 60. LaTeX Warning: Citation `ll' on page 28 undefined on input line 61. [28] LaTeX Warning: Reference `eq:ion' on page 29 undefined on input line 90. LaTeX Warning: Reference `eq:crossinv' on page 29 undefined on input line 100. LaTeX Warning: Reference `eq:crossinv' on page 29 undefined on input line 104. LaTeX Warning: Reference `eq:free' on page 29 undefined on input line 105. LaTeX Warning: Reference `eq:crossinv' on page 29 undefined on input line 105. LaTeX Warning: Reference `eq:free' on page 29 undefined on input line 106. [29] LaTeX Warning: Reference `eq:emissivity' on page 30 undefined on input line 123 . LaTeX Warning: Reference `eq:cons' on page 30 undefined on input line 123. LaTeX Warning: Reference `eq:emissivity' on page 30 undefined on input line 124 . [30] LaTeX Warning: Reference `eq:finalab' on page 31 undefined on input line 135. LaTeX Warning: Reference `eq:finalab' on page 31 undefined on input line 139. LaTeX Warning: Reference `eq:finalem' on page 31 undefined on input line 139. LaTeX Warning: Citation `RL' on page 31 undefined on input line 148. Overfull \hbox (2.70871pt too wide) in paragraph at lines 148--149 \OT1/cmr/m/n/14.4 the sub-script E means "emit-ter", sub-script A means "ab-sor ber"), [31] LaTeX Warning: Citation `ll' on page 32 undefined on input line 154. LaTeX Warning: Reference `eq:mg12' on page 32 undefined on input line 165. LaTeX Warning: Citation `ll' on page 32 undefined on input line 165. [32] Overfull \hbox (2.4854pt too wide) detected at line 174 []\OML/cmm/m/it/14.4 E[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T[]\OT1/cmr/m/n/1 4.4 ) = [][] [] = \OML/cmm/m/it/14.4 T[][] [][] []: LaTeX Warning: Reference `eqmg14' on page 33 undefined on input line 180. LaTeX Warning: Reference `eqmg15' on page 33 undefined on input line 189. Overfull \hbox (18.52773pt too wide) in paragraph at lines 197--197 []\OT1/cmr/bx/n/17.28 Reduction of the multi-group dif-fu-sion equa- )) [33] [34] (./HEDP_Appendixes.tex (./FermiFunction.tex LaTeX Warning: Citation `mcleod' on page 35 undefined on input line 7. LaTeX Warning: Citation `mcleod' on page 35 undefined on input line 12. Overfull \hbox (8.44669pt too wide) in paragraph at lines 15--17 \OT1/cmr/m/n/14.4 is only used for $\OML/cmm/m/it/14.4 g[] \OMS/cmsy/m/n/14.4 2 \OT1/cmr/m/n/14.4 [\OML/cmm/m/it/14.4 e[]\OT1/cmr/m/n/14.4 ; 1)$, be-cause it con-verges when $\OMS/cmsy/m/n/14.4 j []\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 g []\OT1/cmr/m/n/14.4 )\OMS/cmsy/m/n/14.4 j \OML/cmm/m/it/14.4 < LaTeX Warning: Citation `mcleod' on page 35 undefined on input line 18. LaTeX Warning: Citation `gradshtein' on page 35 undefined on input line 26. [35] LaTeX Warning: Citation `gradshtein' on page 36 undefined on input line 45. LaTeX Warning: Citation `mcleod' on page 36 undefined on input line 49. Overfull \hbox (22.54443pt too wide) in paragraph at lines 56--57 [][] ) (./PartitionFunction.tex [36] [37 <./FermiFunctionFig.pdf>]) (./DebyeHuekel.tex Overfull \hbox (5.14973pt too wide) in paragraph at lines 3--3 []\OT1/cmr/bx/n/17.28 Appendix C: Debye-Huekel ap-prox-i-ma-tion [38] LaTeX Warning: Citation `ll' on page 39 undefined on input line 10. LaTeX Warning: Reference `equili' on page 39 undefined on input line 14. LaTeX Warning: Reference `MadS' on page 39 undefined on input line 26. LaTeX Warning: Reference `ni' on page 39 undefined on input line 26. [39] LaTeX Warning: Reference `RDdef' on page 40 undefined on input line 37. LaTeX Warning: Reference `diffstruct' on page 40 undefined on input line 44. Overfull \hbox (52.77228pt too wide) detected at line 50 \OML/cmm/m/it/14.4 A[] \OT1/cmr/m/n/14.4 = \OMS/cmsy/m/n/14.4 h\OML/cmm/m/it/14 .4 ^^N[]i\OMS/cmsy/m/n/14.4 i \OT1/cmr/m/n/14.4 + \OML/cmm/m/it/14.4 ZR[] \OT1/ cmr/m/n/14.4 + []\OML/cmm/m/it/14.4 ; A[] \OT1/cmr/m/n/14.4 = \OML/cmm/m/it/14 .4 Z \OT1/cmr/m/n/14.4 + []\OML/cmm/m/it/14.4 ; LaTeX Warning: Reference `DH' on page 40 undefined on input line 59. LaTeX Warning: Reference `equile' on page 40 undefined on input line 60. [40] LaTeX Warning: Reference `pfDH' on page 41 undefined on input line 74. LaTeX Warning: Reference `FDH' on page 41 undefined on input line 76. (./ionization_table6.tex) Overfull \hbox (335.19704pt too wide) in paragraph at lines 3--107 [] [41]) (./NTemperature.tex Overfull \hbox (24.84813pt too wide) in paragraph at lines 9--16 \OT1/cmr/m/n/14.4 ma-trix, which is sym-met-ric, def-i-nite pos-i-tive and diag onal-dominant. [42] LaTeX Warning: Reference `gov' on page 43 undefined on input line 39. [43] LaTeX Warning: Reference `sym' on page 44 undefined on input line 54. LaTeX Warning: Reference `gov' on page 44 undefined on input line 56. LaTeX Warning: Reference `gov' on page 44 undefined on input line 62. [44] LaTeX Warning: Reference `sem' on page 45 undefined on input line 86. LaTeX Warning: Reference `sem' on page 45 undefined on input line 100. LaTeX Warning: Reference `lin' on page 45 undefined on input line 110. [45] LaTeX Warning: Reference `pos' on page 46 undefined on input line 129. LaTeX Warning: Reference `pos' on page 46 undefined on input line 134. LaTeX Warning: Reference `sym' on page 46 undefined on input line 134. LaTeX Warning: Reference `lin' on page 46 undefined on input line 145. LaTeX Warning: Reference `sem' on page 46 undefined on input line 146. LaTeX Warning: Reference `sem' on page 46 undefined on input line 146. Overfull \hbox (25.82208pt too wide) in paragraph at lines 145--148 []\OT1/cmr/m/n/14.4 Finally, we show how to em-ploy $\OT1/cmr/bx/n/14.4 T[]$ \O T1/cmr/m/n/14.4 found from non-conservative LaTeX Warning: Reference `con' on page 46 undefined on input line 154. [46] [47] [48 <./HeatConductionFig.pdf>] LaTeX Warning: Reference `alg' on page 49 undefined on input line 180. Overfull \hbox (10.57777pt too wide) in paragraph at lines 178--182 \OT1/cmr/m/n/14.4 in-dex, $\OML/cmm/m/it/14.4 L$\OT1/cmr/m/n/14.4 , the Lip-shi tz deriva-tive is $\OML/cmm/m/it/14.4 T[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T[]; T[]\OT1/cmr/m/n/14.4 ) = \OML/cmm/m/it/14.4 a [][] []$\OT1/cmr/m/n/14.4 . LaTeX Warning: Reference `alg' on page 49 undefined on input line 197. [49] LaTeX Warning: Reference `MN' on page 50 undefined on input line 224. LaTeX Warning: Reference `NM' on page 50 undefined on input line 228. LaTeX Warning: Reference `NM' on page 50 undefined on input line 232. LaTeX Warning: Reference `alg' on page 50 undefined on input line 232. Overfull \hbox (51.47855pt too wide) in alignment at lines 233--237 [][][] [] LaTeX Warning: Reference `alg' on page 50 undefined on input line 239. [50] LaTeX Warning: Reference `con' on page 51 undefined on input line 248. )) [51] [52] Underfull \hbox (badness 2285) in paragraph at lines 111--114 []\OT1/cmr/m/n/14.4 J.Bauche, C.Bauche-Arnoult, O.Peyrusse, A.Bachelier, Underfull \hbox (badness 2126) in paragraph at lines 115--119 \OT1/cmr/m/n/14.4 E.Minguez. Rel-a-tivis-tic quan-tum me-chanic cal-cu-la-tion [53] Underfull \hbox (badness 10000) in paragraph at lines 124--127 []\OT1/cmr/m/n/14.4 A.Bar-Shalom, J.Oreg, W.H.Goldstein, D.Shvarts, Underfull \hbox (badness 5316) in paragraph at lines 124--127 \OT1/cmr/m/n/14.4 A.Zigler. Super-transition-arrays: A model for the Underfull \hbox (badness 10000) in paragraph at lines 149--150 []\OT1/cmr/m/n/14.4 NIST Atomic Spec-tra Database. Underfull \hbox (badness 10000) in paragraph at lines 149--150 \OT1/cmr/m/n/14.4 http://physics.nist.gov/PhysRefData/ASD/index.html, [54] Underfull \hbox (badness 1231) in paragraph at lines 161--164 []\OT1/cmr/m/n/14.4 T.A. Carl-son, C.W. Nestor, N. Jr. Wasser-man, J.D. [55] [56] (./HEDP.aux (./HEDP_Part1.aux) (./HEDP_Part2.aux) (./HEDP_Appendixes.aux)) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on HEDP.pdf (56 pages, 396582 bytes). Transcript written on HEDP.log. makeindex HEDP.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file HEDP.idx...done (0 entries accepted, 0 rejected). Nothing written in HEDP.ind. Transcript written in HEDP.ilg. pdflatex HEDP.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./HEDP.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) LaTeX Warning: Unused global option(s): [english]. (./HEDP.aux (./HEDP_Part1.aux) (./HEDP_Part2.aux) (./HEDP_Appendixes.aux)) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) LaTeX Warning: No \author given. [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./HEDP_Part1.tex (./FermiStatistics.tex [3] [4] [5] [6] Overfull \hbox (32.89856pt too wide) detected at line 192 \OMS/cmsy/m/n/12 E \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 ^^@[] [] \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 + \OMS/cmsy/m/n/12 E[]\OML/cmm/m/it/12 ; \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 = []\OML/cmm/m/it/12 Tn[]; \OMS/cmsy/m/ n/12 E[] \OT1/cmr/m/n/12 = \OML/cmm/m/it/12 n[] [] ; [7] [8]) (./Coulomb.tex Overfull \hbox (8.76778pt too wide) in paragraph at lines 3--3 []\OT1/cmr/bx/n/17.28 Madelung ap-prox-i-ma-tion of elec-tro-static en- [9] [10] [11] Overfull \hbox (15.74991pt too wide) detected at line 127 []\OMS/cmsy/m/n/12 E \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 ^^@[] [] \OT1/cmr/m/n/1 2 = \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 + \OMS/cmsy/m/n/12 E[]\OML/cmm/m/it/12 ; \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 = []\OML/cmm/m/it/12 Tn[]; \OMS/cmsy/ m/n/12 E[] \OT1/cmr/m/n/12 = \OML/cmm/m/it/12 n[] [] ; [12] [13] (./ionization_table7.tex) Overfull \hbox (85.39262pt too wide) in paragraph at lines 3--191 [] [14]) (./Excitation.tex [15]) (./PressureIonization.tex [16] Overfull \hbox (32.54692pt too wide) detected at line 107 \OMS/cmsy/m/n/12 ^^@[]h\OML/cmm/m/it/12 ^^N[]^^NE\OMS/cmsy/m/n/12 i \OT1/cmr/m/ n/12 = \OMS/cmsy/m/n/12 ^^@[]h\OML/cmm/m/it/12 ^^N[]^^N\OMS/cmsy/m/n/12 h\OML/c mm/m/it/12 E\OMS/cmsy/m/n/12 i[]i[] ^^@ []hh\OML/cmm/m/it/12 ^^NE[]^^N[]\OMS/cm sy/m/n/12 i[]i[] ^^@ []h\OML/cmm/m/it/12 ^^N\OMS/cmsy/m/n/12 h[]i[]\OML/cmm/m/i t/12 ^^N\OMS/cmsy/m/n/12 h\OML/cmm/m/it/12 E\OMS/cmsy/m/n/12 i[]i[]\OML/cmm/m/i t/12 : )) [17] (./HEDP_Part2.tex (./MultiGroup.tex Overfull \hbox (50.42183pt too wide) detected at line 38 [][] \OT1/cmr/m/n/14.4 + \OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/m/n/14.4 ([]\OML/cmm /m/it/14.4 E[]\OT1/cmr/m/n/14.4 ) \OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 (\OM L/cmm/m/it/14.4 ^^M[] \OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 1)(\OMS/cmsy/m/n /14.4 r ^^A \OT1/cmr/bx/n/14.4 u\OT1/cmr/m/n/14.4 )\OML/cmm/m/it/14.4 "[] \OT1/ cmr/m/n/14.4 = []\OML/cmm/m/it/14.4 : [18] Overfull \hbox (21.41643pt too wide) in alignment at lines 70--85 [][][] [] [19] Overfull \hbox (108.69894pt too wide) in alignment at lines 88--102 [][][] [] [20] Overfull \hbox (67.79787pt too wide) detected at line 130 [][] \OT1/cmr/m/n/14.4 + \OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/m/n/14.4 (\OT1/cmr/b x/n/14.4 u\OML/cmm/m/it/14.4 E\OT1/cmr/m/n/14.4 ) + (\OML/cmm/m/it/14.4 ^^M[] \ OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 1)(\OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/bx /n/14.4 u\OT1/cmr/m/n/14.4 )\OML/cmm/m/it/14.4 E \OT1/cmr/m/n/14.4 = [][] []\OM L/cmm/m/it/14.4 : [21] Overfull \hbox (113.17989pt too wide) in alignment at lines 141--144 [][][] [] [22] [23] [24] Overfull \hbox (94.64406pt too wide) detected at line 221 []\OML/cmm/m/it/14.4 N[] \OMS/cmsy/m/n/14.4 / \OML/cmm/m/it/14.4 g[] []\OT1/cmr /m/n/14.4 [\OMS/cmsy/m/n/14.4 ^^@\OML/cmm/m/it/14.4 E[]=\OT1/cmr/m/n/14.4 (\OML /cmm/m/it/14.4 k[]T\OT1/cmr/m/n/14.4 )]\OML/cmm/m/it/14.4 ; [] \OT1/cmr/m/n/14 .4 = [] [] = [][\OMS/cmsy/m/n/14.4 ^^@\OML/cmm/m/it/14.4 "=\OT1/cmr/m/n/14.4 (\ OML/cmm/m/it/14.4 k[]T\OT1/cmr/m/n/14.4 )] Overfull \hbox (5.53162pt too wide) in paragraph at lines 226--228 \OT1/cmr/m/n/14.4 where the ef-fec-tive ab-sorp-tion co-ef-fi-cient, $\OML/cmm/ m/it/14.4 a[]$\OT1/cmr/m/n/14.4 , is in-dro-duced, which [25] Overfull \hbox (28.41185pt too wide) detected at line 243 []\OML/cmm/m/it/14.4 E[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T; "\OT1/cmr/m/n/ 14.4 ) = \OML/cmm/m/it/14.4 T[][][][]; \OT1/cmr/m/n/14.4 = []\OML/cmm/m/it/ 14.4 ; x \OT1/cmr/m/n/14.4 = []\OML/cmm/m/it/14.4 : (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd)) (./PhotoIonization.tex [26] [27] [28] Overfull \hbox (5.29059pt too wide) in paragraph at lines 100--108 []\OT1/cmr/m/n/14.4 The rule as in Eq.(104[]) ex-presses the so-called \OT1/cmr /m/it/14.4 cross-invariance [29] [30] LaTeX Warning: Citation `RL' on page 31 undefined on input line 148. Overfull \hbox (2.70871pt too wide) in paragraph at lines 148--149 \OT1/cmr/m/n/14.4 the sub-script E means "emit-ter", sub-script A means "ab-sor ber"), [31] [32] Overfull \hbox (2.4854pt too wide) detected at line 174 []\OML/cmm/m/it/14.4 E[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T[]\OT1/cmr/m/n/1 4.4 ) = [][] [] = \OML/cmm/m/it/14.4 T[][] [][] []: Overfull \hbox (18.52773pt too wide) in paragraph at lines 197--197 []\OT1/cmr/bx/n/17.28 Reduction of the multi-group dif-fu-sion equa- )) [33] [34] (./HEDP_Appendixes.tex (./FermiFunction.tex Overfull \hbox (8.44669pt too wide) in paragraph at lines 15--17 \OT1/cmr/m/n/14.4 is only used for $\OML/cmm/m/it/14.4 g[] \OMS/cmsy/m/n/14.4 2 \OT1/cmr/m/n/14.4 [\OML/cmm/m/it/14.4 e[]\OT1/cmr/m/n/14.4 ; 1)$, be-cause it con-verges when $\OMS/cmsy/m/n/14.4 j []\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 g []\OT1/cmr/m/n/14.4 )\OMS/cmsy/m/n/14.4 j \OML/cmm/m/it/14.4 < [35] Overfull \hbox (22.54443pt too wide) in paragraph at lines 56--57 [][] ) (./PartitionFunction.tex [36] [37 <./FermiFunctionFig.pdf>]) (./DebyeHuekel.tex Overfull \hbox (5.14973pt too wide) in paragraph at lines 3--3 []\OT1/cmr/bx/n/17.28 Appendix C: Debye-Huekel ap-prox-i-ma-tion [38] [39] Overfull \hbox (52.77228pt too wide) detected at line 50 \OML/cmm/m/it/14.4 A[] \OT1/cmr/m/n/14.4 = \OMS/cmsy/m/n/14.4 h\OML/cmm/m/it/14 .4 ^^N[]i\OMS/cmsy/m/n/14.4 i \OT1/cmr/m/n/14.4 + \OML/cmm/m/it/14.4 ZR[] \OT1/ cmr/m/n/14.4 + []\OML/cmm/m/it/14.4 ; A[] \OT1/cmr/m/n/14.4 = \OML/cmm/m/it/14 .4 Z \OT1/cmr/m/n/14.4 + []\OML/cmm/m/it/14.4 ; [40] (./ionization_table6.tex) Overfull \hbox (335.19704pt too wide) in paragraph at lines 3--107 [] [41]) (./NTemperature.tex Overfull \hbox (24.84813pt too wide) in paragraph at lines 9--16 \OT1/cmr/m/n/14.4 ma-trix, which is sym-met-ric, def-i-nite pos-i-tive and diag onal-dominant. [42] [43] [44] [45] Overfull \hbox (25.82208pt too wide) in paragraph at lines 145--148 []\OT1/cmr/m/n/14.4 Finally, we show how to em-ploy $\OT1/cmr/bx/n/14.4 T[]$ \O T1/cmr/m/n/14.4 found from non-conservative [46] [47] [48 <./HeatConductionFig.pdf>] Overfull \hbox (10.57777pt too wide) in paragraph at lines 178--182 \OT1/cmr/m/n/14.4 in-dex, $\OML/cmm/m/it/14.4 L$\OT1/cmr/m/n/14.4 , the Lip-shi tz deriva-tive is $\OML/cmm/m/it/14.4 T[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T[]; T[]\OT1/cmr/m/n/14.4 ) = \OML/cmm/m/it/14.4 a [][] []$\OT1/cmr/m/n/14.4 . [49] Overfull \hbox (51.47855pt too wide) in alignment at lines 233--237 [][][] [] [50])) [51] [52] Underfull \hbox (badness 2285) in paragraph at lines 111--114 []\OT1/cmr/m/n/14.4 J.Bauche, C.Bauche-Arnoult, O.Peyrusse, A.Bachelier, Underfull \hbox (badness 2126) in paragraph at lines 115--119 \OT1/cmr/m/n/14.4 E.Minguez. Rel-a-tivis-tic quan-tum me-chanic cal-cu-la-tion [53] Underfull \hbox (badness 10000) in paragraph at lines 124--127 []\OT1/cmr/m/n/14.4 A.Bar-Shalom, J.Oreg, W.H.Goldstein, D.Shvarts, Underfull \hbox (badness 5316) in paragraph at lines 124--127 \OT1/cmr/m/n/14.4 A.Zigler. Super-transition-arrays: A model for the Underfull \hbox (badness 10000) in paragraph at lines 149--150 []\OT1/cmr/m/n/14.4 NIST Atomic Spec-tra Database. Underfull \hbox (badness 10000) in paragraph at lines 149--150 \OT1/cmr/m/n/14.4 http://physics.nist.gov/PhysRefData/ASD/index.html, [54] Underfull \hbox (badness 1231) in paragraph at lines 161--164 []\OT1/cmr/m/n/14.4 T.A. Carl-son, C.W. Nestor, N. Jr. Wasser-man, J.D. [55] [56] (./HEDP.aux (./HEDP_Part1.aux) (./HEDP_Part2.aux) (./HEDP_Appendixes.aux)) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information) Output written on HEDP.pdf (56 pages, 394890 bytes). Transcript written on HEDP.log. makeindex HEDP.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file HEDP.idx...done (0 entries accepted, 0 rejected). Nothing written in HEDP.ind. Transcript written in HEDP.ilg. pdflatex HEDP.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./HEDP.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) LaTeX Warning: Unused global option(s): [english]. (./HEDP.aux (./HEDP_Part1.aux) (./HEDP_Part2.aux) (./HEDP_Appendixes.aux)) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) LaTeX Warning: No \author given. [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./HEDP_Part1.tex (./FermiStatistics.tex [3] [4] [5] [6] Overfull \hbox (32.89856pt too wide) detected at line 192 \OMS/cmsy/m/n/12 E \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 ^^@[] [] \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 + \OMS/cmsy/m/n/12 E[]\OML/cmm/m/it/12 ; \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 = []\OML/cmm/m/it/12 Tn[]; \OMS/cmsy/m/ n/12 E[] \OT1/cmr/m/n/12 = \OML/cmm/m/it/12 n[] [] ; [7] [8]) (./Coulomb.tex Overfull \hbox (8.76778pt too wide) in paragraph at lines 3--3 []\OT1/cmr/bx/n/17.28 Madelung ap-prox-i-ma-tion of elec-tro-static en- [9] [10] [11] Overfull \hbox (15.74991pt too wide) detected at line 127 []\OMS/cmsy/m/n/12 E \OT1/cmr/m/n/12 = \OMS/cmsy/m/n/12 ^^@[] [] \OT1/cmr/m/n/1 2 = \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 + \OMS/cmsy/m/n/12 E[]\OML/cmm/m/it/12 ; \OMS/cmsy/m/n/12 E[] \OT1/cmr/m/n/12 = []\OML/cmm/m/it/12 Tn[]; \OMS/cmsy/ m/n/12 E[] \OT1/cmr/m/n/12 = \OML/cmm/m/it/12 n[] [] ; [12] [13] (./ionization_table7.tex) Overfull \hbox (85.39262pt too wide) in paragraph at lines 3--191 [] [14]) (./Excitation.tex [15]) (./PressureIonization.tex [16] Overfull \hbox (32.54692pt too wide) detected at line 107 \OMS/cmsy/m/n/12 ^^@[]h\OML/cmm/m/it/12 ^^N[]^^NE\OMS/cmsy/m/n/12 i \OT1/cmr/m/ n/12 = \OMS/cmsy/m/n/12 ^^@[]h\OML/cmm/m/it/12 ^^N[]^^N\OMS/cmsy/m/n/12 h\OML/c mm/m/it/12 E\OMS/cmsy/m/n/12 i[]i[] ^^@ []hh\OML/cmm/m/it/12 ^^NE[]^^N[]\OMS/cm sy/m/n/12 i[]i[] ^^@ []h\OML/cmm/m/it/12 ^^N\OMS/cmsy/m/n/12 h[]i[]\OML/cmm/m/i t/12 ^^N\OMS/cmsy/m/n/12 h\OML/cmm/m/it/12 E\OMS/cmsy/m/n/12 i[]i[]\OML/cmm/m/i t/12 : )) [17] (./HEDP_Part2.tex (./MultiGroup.tex Overfull \hbox (50.42183pt too wide) detected at line 38 [][] \OT1/cmr/m/n/14.4 + \OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/m/n/14.4 ([]\OML/cmm /m/it/14.4 E[]\OT1/cmr/m/n/14.4 ) \OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 (\OM L/cmm/m/it/14.4 ^^M[] \OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 1)(\OMS/cmsy/m/n /14.4 r ^^A \OT1/cmr/bx/n/14.4 u\OT1/cmr/m/n/14.4 )\OML/cmm/m/it/14.4 "[] \OT1/ cmr/m/n/14.4 = []\OML/cmm/m/it/14.4 : [18] Overfull \hbox (21.41643pt too wide) in alignment at lines 70--85 [][][] [] [19] Overfull \hbox (108.69894pt too wide) in alignment at lines 88--102 [][][] [] [20] Overfull \hbox (67.79787pt too wide) detected at line 130 [][] \OT1/cmr/m/n/14.4 + \OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/m/n/14.4 (\OT1/cmr/b x/n/14.4 u\OML/cmm/m/it/14.4 E\OT1/cmr/m/n/14.4 ) + (\OML/cmm/m/it/14.4 ^^M[] \ OMS/cmsy/m/n/14.4 ^^@ \OT1/cmr/m/n/14.4 1)(\OMS/cmsy/m/n/14.4 r ^^A \OT1/cmr/bx /n/14.4 u\OT1/cmr/m/n/14.4 )\OML/cmm/m/it/14.4 E \OT1/cmr/m/n/14.4 = [][] []\OM L/cmm/m/it/14.4 : [21] Overfull \hbox (113.17989pt too wide) in alignment at lines 141--144 [][][] [] [22] [23] [24] Overfull \hbox (94.64406pt too wide) detected at line 221 []\OML/cmm/m/it/14.4 N[] \OMS/cmsy/m/n/14.4 / \OML/cmm/m/it/14.4 g[] []\OT1/cmr /m/n/14.4 [\OMS/cmsy/m/n/14.4 ^^@\OML/cmm/m/it/14.4 E[]=\OT1/cmr/m/n/14.4 (\OML /cmm/m/it/14.4 k[]T\OT1/cmr/m/n/14.4 )]\OML/cmm/m/it/14.4 ; [] \OT1/cmr/m/n/14 .4 = [] [] = [][\OMS/cmsy/m/n/14.4 ^^@\OML/cmm/m/it/14.4 "=\OT1/cmr/m/n/14.4 (\ OML/cmm/m/it/14.4 k[]T\OT1/cmr/m/n/14.4 )] Overfull \hbox (5.53162pt too wide) in paragraph at lines 226--228 \OT1/cmr/m/n/14.4 where the ef-fec-tive ab-sorp-tion co-ef-fi-cient, $\OML/cmm/ m/it/14.4 a[]$\OT1/cmr/m/n/14.4 , is in-dro-duced, which [25] Overfull \hbox (28.41185pt too wide) detected at line 243 []\OML/cmm/m/it/14.4 E[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T; "\OT1/cmr/m/n/ 14.4 ) = \OML/cmm/m/it/14.4 T[][][][]; \OT1/cmr/m/n/14.4 = []\OML/cmm/m/it/ 14.4 ; x \OT1/cmr/m/n/14.4 = []\OML/cmm/m/it/14.4 : (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd)) (./PhotoIonization.tex [26] [27] [28] Overfull \hbox (5.29059pt too wide) in paragraph at lines 100--108 []\OT1/cmr/m/n/14.4 The rule as in Eq.(104[]) ex-presses the so-called \OT1/cmr /m/it/14.4 cross-invariance [29] [30] LaTeX Warning: Citation `RL' on page 31 undefined on input line 148. Overfull \hbox (2.70871pt too wide) in paragraph at lines 148--149 \OT1/cmr/m/n/14.4 the sub-script E means "emit-ter", sub-script A means "ab-sor ber"), [31] [32] Overfull \hbox (2.4854pt too wide) detected at line 174 []\OML/cmm/m/it/14.4 E[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T[]\OT1/cmr/m/n/1 4.4 ) = [][] [] = \OML/cmm/m/it/14.4 T[][] [][] []: Overfull \hbox (18.52773pt too wide) in paragraph at lines 197--197 []\OT1/cmr/bx/n/17.28 Reduction of the multi-group dif-fu-sion equa- )) [33] [34] (./HEDP_Appendixes.tex (./FermiFunction.tex Overfull \hbox (8.44669pt too wide) in paragraph at lines 15--17 \OT1/cmr/m/n/14.4 is only used for $\OML/cmm/m/it/14.4 g[] \OMS/cmsy/m/n/14.4 2 \OT1/cmr/m/n/14.4 [\OML/cmm/m/it/14.4 e[]\OT1/cmr/m/n/14.4 ; 1)$, be-cause it con-verges when $\OMS/cmsy/m/n/14.4 j []\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 g []\OT1/cmr/m/n/14.4 )\OMS/cmsy/m/n/14.4 j \OML/cmm/m/it/14.4 < [35] Overfull \hbox (22.54443pt too wide) in paragraph at lines 56--57 [][] ) (./PartitionFunction.tex [36] [37 <./FermiFunctionFig.pdf>]) (./DebyeHuekel.tex Overfull \hbox (5.14973pt too wide) in paragraph at lines 3--3 []\OT1/cmr/bx/n/17.28 Appendix C: Debye-Huekel ap-prox-i-ma-tion [38] [39] Overfull \hbox (52.77228pt too wide) detected at line 50 \OML/cmm/m/it/14.4 A[] \OT1/cmr/m/n/14.4 = \OMS/cmsy/m/n/14.4 h\OML/cmm/m/it/14 .4 ^^N[]i\OMS/cmsy/m/n/14.4 i \OT1/cmr/m/n/14.4 + \OML/cmm/m/it/14.4 ZR[] \OT1/ cmr/m/n/14.4 + []\OML/cmm/m/it/14.4 ; A[] \OT1/cmr/m/n/14.4 = \OML/cmm/m/it/14 .4 Z \OT1/cmr/m/n/14.4 + []\OML/cmm/m/it/14.4 ; [40] (./ionization_table6.tex) Overfull \hbox (335.19704pt too wide) in paragraph at lines 3--107 [] [41]) (./NTemperature.tex Overfull \hbox (24.84813pt too wide) in paragraph at lines 9--16 \OT1/cmr/m/n/14.4 ma-trix, which is sym-met-ric, def-i-nite pos-i-tive and diag onal-dominant. [42] [43] [44] [45] Overfull \hbox (25.82208pt too wide) in paragraph at lines 145--148 []\OT1/cmr/m/n/14.4 Finally, we show how to em-ploy $\OT1/cmr/bx/n/14.4 T[]$ \O T1/cmr/m/n/14.4 found from non-conservative [46] [47] [48 <./HeatConductionFig.pdf>] Overfull \hbox (10.57777pt too wide) in paragraph at lines 178--182 \OT1/cmr/m/n/14.4 in-dex, $\OML/cmm/m/it/14.4 L$\OT1/cmr/m/n/14.4 , the Lip-shi tz deriva-tive is $\OML/cmm/m/it/14.4 T[]\OT1/cmr/m/n/14.4 (\OML/cmm/m/it/14.4 T[]; T[]\OT1/cmr/m/n/14.4 ) = \OML/cmm/m/it/14.4 a [][] []$\OT1/cmr/m/n/14.4 . [49] Overfull \hbox (51.47855pt too wide) in alignment at lines 233--237 [][][] [] [50])) [51] [52] Underfull \hbox (badness 2285) in paragraph at lines 111--114 []\OT1/cmr/m/n/14.4 J.Bauche, C.Bauche-Arnoult, O.Peyrusse, A.Bachelier, Underfull \hbox (badness 2126) in paragraph at lines 115--119 \OT1/cmr/m/n/14.4 E.Minguez. Rel-a-tivis-tic quan-tum me-chanic cal-cu-la-tion [53] Underfull \hbox (badness 10000) in paragraph at lines 124--127 []\OT1/cmr/m/n/14.4 A.Bar-Shalom, J.Oreg, W.H.Goldstein, D.Shvarts, Underfull \hbox (badness 5316) in paragraph at lines 124--127 \OT1/cmr/m/n/14.4 A.Zigler. Super-transition-arrays: A model for the Underfull \hbox (badness 10000) in paragraph at lines 149--150 []\OT1/cmr/m/n/14.4 NIST Atomic Spec-tra Database. Underfull \hbox (badness 10000) in paragraph at lines 149--150 \OT1/cmr/m/n/14.4 http://physics.nist.gov/PhysRefData/ASD/index.html, [54] Underfull \hbox (badness 1231) in paragraph at lines 161--164 []\OT1/cmr/m/n/14.4 T.A. Carl-son, C.W. Nestor, N. Jr. Wasser-man, J.D. [55] [56] (./HEDP.aux (./HEDP_Part1.aux) (./HEDP_Part2.aux) (./HEDP_Appendixes.aux)) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information) Output written on HEDP.pdf (56 pages, 394890 bytes). Transcript written on HEDP.log. mv HEDP.pdf ../ rm -f HEDP.ind HEDP.idx HEDP.ilg make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/CRASH/doc/Tex' make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/Doc/Tex' rm -rf *.aux *.log *.toc *.dvi *.ind *.idx *~ ../../PARAM.xmltex cd ..; rm -rf USERMANUAL.pdf DESIGN.pdf STANDARDS.pdf make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/Doc/Tex' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/Doc/Tex' /homedata/gtoth/SWMFTEST/SWMF/share/Scripts/XmlToTex.pl ../../PARAM.XML > ../../PARAM.xmltex touch USERMANUAL.ind USERMANUAL.idx pdflatex USERMANUAL.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./USERMANUAL.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) No file USERMANUAL.aux. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] No file USERMANUAL.toc. (./introduction.tex [3] [4] Chapter 1. Underfull \vbox (badness 5970) has occurred while \output is active [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)) [6] Chapter 2. (./quickstart.tex (../../README.md Overfull \hbox (47.44444pt too wide) in paragraph at lines 24--24 [][] Overfull \hbox (63.64442pt too wide) in paragraph at lines 26--26 [][] [7] Underfull \vbox (badness 10000) has occurred while \output is active [8] Underfull \vbox (badness 10000) has occurred while \output is active [9]) [10] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [11] [12] [13] [14] [15] [16] LaTeX Warning: Reference `section:idl_visualization' on page 17 undefined on in put line 526. LaTeX Warning: Reference `section:tecplot_visualization' on page 17 undefined o n input line 527. [17]) (./hardware_software.tex LaTeX Warning: Reference `section:main_make' on page 18 undefined on input line 22. LaTeX Warning: Reference `tab:memory' on page 18 undefined on input line 58. LaTeX Warning: Reference `section:compiler_flags' on page 18 undefined on input line 65. [18]) (./installation.tex [19] Overfull \hbox (4.24501pt too wide) in paragraph at lines 47--47 [] \OT1/pcr/m/n/10 ConvertRestart.pl Script to convert the endiannes s of restart files[] [20] LaTeX Warning: Reference `section:ncells' on page 21 undefined on input line 14 6. LaTeX Warning: Reference `fig:stretched_initial_grid' on page 21 undefined on i nput line 172. [21] Underfull \vbox (badness 4686) has occurred while \output is active [22 <./proc _dims.pdf>] [23] LaTeX Warning: Reference `section:compiler' on page 24 undefined on input line 323. LaTeX Warning: Reference `section:main_make' on page 24 undefined on input line 325. [24] LaTeX Warning: Reference `chapter:param' on page 25 undefined on input line 445 . ) (./runs.tex [25] LaTeX Warning: Reference `section:main_make' on page 26 undefined on input line 16. LaTeX Warning: Reference `chapter:param' on page 26 undefined on input line 28. Overfull \hbox (3.43063pt too wide) in paragraph at lines 41--48 \OT1/ptm/m/n/10 scrip-tion given in the PARAM.XML (or the PARAM.pl file on sys- tems which do not have the XML-PARSER::EasyTree [26] LaTeX Warning: Reference `section:main_make' on page 27 undefined on input line 90. LaTeX Warning: Reference `section:main_make' on page 27 undefined on input line 100. ) [27] [28] Chapter 3. (./param.tex [29] [30] [31] [32] LaTeX Warning: Reference `section:order' on page 33 undefined on input line 334 . [33] [34] Underfull \vbox (badness 10000) has occurred while \output is active [35] [36]) (../../PARAM.xmltex Underfull \vbox (badness 4765) has occurred while \output is active [37] [38] [39] Overfull \hbox (59.77959pt too wide) in paragraph at lines 160--163 []\OT1/ptm/m/n/10 The Tol-er-ance pa-ram-e-ter sets if the it-er-a-tive so-lu-t ion Witer is close enough to W, abs(W-Witer).le.Tolerance*[abs(W)+abs(Witer)], [40] Overfull \hbox (4.24501pt too wide) in paragraph at lines 300--300 []\OT1/pcr/m/n/10 NEW NamePlanet (rest of parameters read f or unknown planet)[] [41] [42] [43] [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 679--686 [46] Overfull \hbox (4.24501pt too wide) in paragraph at lines 693--693 []\OT1/pcr/m/n/10 F DoDebugGhost (parameter for show_B LK in library.f90)[] [47] [48] [49] [50] [51] [52] [53] [54] [55] Overfull \hbox (3.87938pt too wide) in paragraph at lines 1411--1415 []\OT1/ptm/m/n/10 The #NEWRESTART com-mand sets the fol-low-ing global vari-abl es: DoRestart=.true. (read restart files), DoRestart- [56] Overfull \hbox (70.24501pt too wide) in paragraph at lines 1475--1475 [] \OT1/pcr/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1475--1475 [] \OT1/pcr/m/n/10 radiative outflow boundaries are applied for radiation energy densities[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 outflow - same as 'float' but the pressure is set to pO utflow from #OUTFLOWPRESSURE[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 reflect - reflective (anti-symmetric for the normal com ponents of V and B,[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 linetied - symmetric for density, anti-symmetric for mom entum, float all others[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 inflow/vary - time dependent boundary based on solar wind i nput file (#SOLARWINDFILE)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 ihbuffer - values obtained from the IH component (this i s set automatically)[] Overfull \hbox (82.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 none - do not change ghost cells. This is useful if the outer boundary is not used.[] [57] Overfull \hbox (8.74103pt too wide) in paragraph at lines 1529--1535 []\OT1/ptm/m/n/10 The outer bound-aries have to be face based if a brick-shaped com-pu-ta-tional do-main is cut out from the sphere/cylinder Overfull \hbox (70.24501pt too wide) in paragraph at lines 1551--1551 [] \OT1/pcr/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1551--1551 [] \OT1/pcr/m/n/10 radiative outflow boundaries are applied for radiation energy densities[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 outflow - same as 'float' but the pressure is set to pO utflow from #OUTFLOWPRESSURE[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflect - reflect the normal component of B1, reflect t he full velocity vector[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflectb - reflect the normal component of full B, refle ct the full velocity vector[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflectall - reflect the normal component of B1 and veloci ty, symmetric for all other[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 fixed - fixed values (set by #SOLARWIND or #BOUNDARYS TATE), total B is set[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 inflow/vary - time dependent boundary based on solar wind i nput file (#SOLARWINDFILE)[] [58] [59] Overfull \hbox (40.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'reflectb' - same as reflect, but the normal component of full B is reflected.[] Overfull \hbox (88.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'outflow' - same as 'float' but the pressure is set t o pOutflow from #OUTFLOWPRESSURE[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'fixed' - use initial solar wind values. Total B is set to solar wind B.[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'fixedb1' - use initial solar wind values. B1 is set is to solar wind B.[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'ionosphere' - reflect velocity relative to corotation + ionosphere ExB drift[] Overfull \hbox (136.24501pt too wide) in paragraph at lines 1697--1697 [] \OT1/pcr/m/n/10 is applied above 55 degrees latitude. Se e #OUTFLOWCRITERIA for more information.[] [60] [61] [62] [63] [64] [65] Overfull \hbox (68.17989pt too wide) in paragraph at lines 2103--2106 \OT1/ptm/m/n/10 TypeCoordSystem de-fines the co-or-di-nate sys-tem for the com- po-nent. The co-or-di-nate sys-tems are de-fined in share/Library/src/CON[]axes . [66] [67] [68] [69] Overfull \hbox (0.18028pt too wide) in paragraph at lines 2491--2493 []\OT1/ptm/m/n/10 If the #SCHEME com-mand is not used, then the de-faults are n Stage=2 with the half-step pre-dic-tor and CflExpl=0.8. [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 2777--2780 Overfull \hbox (6.39099pt too wide) in paragraph at lines 2822--2827 []\OT1/ptm/m/n/10 For steady state run the de-fault is the back-ward Eu-ler sch eme, which cor-re-sponds to Im-plCo-eff=1.0 and UsedBdf2=F. [74] [75] Overfull \hbox (4.24501pt too wide) in paragraph at lines 2971--2971 []\OT1/pcr/m/n/10 MBILU TypePrecond (MBILU, BILU, DILU, GS, BLOCKJACO BI, JACOBI, HYPRE)[] [76] [77] [78] [79] Overfull \hbox (73.71059pt too wide) in paragraph at lines 3226--3233 \OT1/ptm/m/n/10 saved only at the end. A bi-nary restart file is pro-duced for ev-ery block and named as RESTARTOUT-DIR/blkGLOBALBLKNUMBER.rst. Overfull \hbox (1.97142pt too wide) in paragraph at lines 3234--3237 []\OT1/ptm/m/n/10 The restart files are over-writ-ten ev-ery time a new restart is done, but one can change the name of the RESTARTOUT- [80] Overfull \hbox (4.48077pt too wide) in paragraph at lines 3290--3293 []\OT1/ptm/m/n/10 The pos-si-ble val-ues for StringLog-Var and the cor-re-spond -ing vari-ables to-gether with the de-fault val-ues for StringLog- Overfull \hbox (46.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 VAR - average of variable VAR (listed in Name Var_V of ModEquation.f90)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Erad Ew - average radiation/wave energy (summed f or all groups/waves)[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Lon1 Lon2 Status - average of longitude and status of fiel dline (for testing)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 VARpnt - point value of VAR (listed in NameVar_V ) at the test cell[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Statuspnt - point value of status of fieldline trac ing from test cell:[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Jinmax Joutmax - maximum of inward and outward currents at rCurrents of #BODY[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Jin Jout - surface integral of inward and outward currents at rCurrents[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Aflx - surface integral of 1 at radii def ined in rLog (area)[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Pvecflx - surface integral of ExB at radii def ined in rLog (Poynting flux)[] Overfull \hbox (40.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Dstflx - surface integral of B1z at radii def ined in rLog (Dst index)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 DstDivb - error of the dstflx integral due to fin ite value of div B[] [81] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3357--3357 [] \OT1/pcr/m/n/10 none - there will be no indication of time in the logfile ( not even the number of steps)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 3357--3357 [] \OT1/pcr/m/n/10 date - date-time as 7 integers: year month day hour minute second millisecond,[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 2011-02-01T00:00:00 UT StringStartTimeTraj ! Read if StringS atellite contains 'trajrange'[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 2011-02-10T00:00:00 UT StringEndTimeTraj ! Read if StringS atellite contains 'trajrange'[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 1 h StringDtTraj ! Read if StringS atellite contains 'trajrange'[] [82] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3460--3460 [] \OT1/pcr/m/n/10 date - date-time as 7 integers: year month day hour minute second millisecond[] [83] Overfull \hbox (28.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 'YYYY MM DD HH MM SS MSC UT' (single digit need t o fill 0 ahead and the[] Overfull \hbox (40.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 sperator ('-', ':', 'T', ' ') between numbers can be whatever characters)[] Overfull \hbox (76.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 Any number followed by ' w'/' d'/' h'/' m'/' s', in which ca se the time is with respect to[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 #STARTTIME. For example, 1 h here means StartTime + 1 hour. THERE IS A SPACE[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 Any number (in which case it is assumed to be in seconds), i n which case the time[] [84] [85] [86] [87] [88] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 1d HD idl_tec StringPlot ! 1d plot (with Tecplot he ader) along X axis[] Underfull \vbox (badness 10000) has occurred while \output is active [89] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 eqr eqr idl StringPlot ! Equatorial (magnetic) fi eld line tracing info[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 20 nRadius ! Starting points on the S M equatorial plane[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 20 nRadius ! Starting points on the S M equatorial plane[] Underfull \vbox (badness 10000) has occurred while \output is active [90] Overfull \hbox (10.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 lcb int tec StringPlot !last closed field line p lots with integrals[] Underfull \vbox (badness 10000) has occurred while \output is active [91] Underfull \vbox (badness 10000) has occurred while \output is active [92] Underfull \vbox (badness 10000) has occurred while \output is active [93] [94] Overfull \hbox (34.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'ray' - vars: bx by bz lon1 lat1 lon2 lat2 status blk (if DoMapEquatorRay=F)[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 vars: bx by bz req1 phi1 req2 phi2 status blk (if DoMapEquatorRay=T)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'eqr' - vars: iLine l x y z rho ux uy uz bx by bz p rCurve (for all rays traced)[] Overfull \hbox (82.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'eqb' - vars: z PrimVarMinB rCurve xZ0 yZ0 zZ0 PrimVarZ0 rCu rveZ0 (B is in SM coordinates)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'pos' - vars x y z (PlotArea='lin' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'sol' - vars: wl pb (PlotArea='los' only)[] Overfull \hbox (94.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'lgq' - vars: squash.03 squash.12 squash.2 squash-15 squash- 2 squash-3 (PlotArea='los' only)[] [95] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'euv' - vars: euv171 euv195 euv284 (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'sxr' - vars: sxr (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'tbl' - vars: listed in the LOS table file (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'dem' - vars: DEM, EM (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'int' - vars: 1/B n/B p/B (PlotArea='lcb' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'nul' - vars: (PlotArea='lcb' only)[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'ins' - vars: determined by the corresponding instrument, se e line-of-sight below[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 - pars: determined by the corresponding instrument, se e line-of-sight below[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 RadiusMin RadiusMax if PlotArea is 'eqr', 'eqb', 'shl', 'sln', 'slg', 'shk'[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 dRadius, dLon, dLat if PlotArea is 'sln', 'slg' or 'shl' and range is nonzero.[] Overfull \hbox (160.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 DxSavePlot if PlotForm is 'idl' and PlotArea is not box/shl/sln/slg/shk/los/rfr/lin/eqr/eqb[] [96] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4372--4372 [] \OT1/pcr/m/n/10 HGI coordinates (SC,IH and OH) or the GM coordinates[] [97] Underfull \hbox (badness 10000) in paragraph at lines 4432--4441 [98] [99] [100] [101] [102] Overfull \hbox (7.63066pt too wide) in paragraph at lines 4767--4773 []\OT1/ptm/m/n/10 The lat-est im-ple-men-ta-tion for the Gibson-Low erup-tive e vent gen-er-a-tor (Type-Cme=GL) fol-lows the pa-per Borovikov, [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] Overfull \hbox (4.24501pt too wide) in paragraph at lines 5679--5679 [] \OT1/pcr/m/n/10 'transient RhoU_dot' - relative change of momentum ( d|rhoU|/dt)/|rhoU|[] [115] [116] Overfull \hbox (2.72028pt too wide) in paragraph at lines 5831--5836 \OT1/ptm/m/n/10 This com-mand is only use-ful if the nOrder is larger than 2 in the #SCHEME com-mand. In this case the StringLowOrder- [117] [118] [119] [120] [121] [122] Overfull \hbox (11.43059pt too wide) in paragraph at lines 6255--6258 []\OT1/ptm/m/n/10 When Us-eSin-gleIon-Ve-loc-ity is true, the ion ve-loc-i-ties are set to the av-er-age fluid ve-loc-ity $\OML/cmm/m/it/10 u \OT1/cmr/m/n/10 = [] []\OML/cmm/m/it/10 s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]su[]s\OT1/cmr/m /n/10 )\OML/cmm/m/it/10 = [] []s^^Z[]s$ Overfull \hbox (65.49863pt too wide) in paragraph at lines 6259--6262 []\OT1/ptm/m/n/10 When Us-eSin-gleIon-Tem-per-a-ture is true, the ion tem-per-a -tures are set to the av-er-age tem-per-a-ture $\OML/cmm/m/it/10 k[]BT \OT1/cmr /m/n/10 = [] []\OML/cmm/m/it/10 sp[]s= [] []s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]s=M[]s\OT1/cmr/m/n/10 )$ Overfull \hbox (4.24501pt too wide) in paragraph at lines 6273--6273 []\OT1/pcr/m/n/10 100.0 uCutOffDim [km/s] read if Tau CutOffDim positive[] [123] Overfull \hbox (61.65004pt too wide) in paragraph at lines 6295--6303 \OT1/ptm/m/n/10 comes large. Set-ting uCut-offDim = -1.0 switches to a physics based cut-off ve-loc-ity which is de-fined as B/sqrt[rho1*rho2/(rho1+rho2)] [124] [125] [126] [127] [128] Overfull \hbox (4.24501pt too wide) in paragraph at lines 6751--6751 []\OT1/pcr/m/n/10 cg TypeProjectIter:'cg' or 'bicgstab' fo r iterative scheme[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 6751--6751 []\OT1/pcr/m/n/10 rel TypeProjectStop:'rel' or 'max' error for stop condition[] [129] [130] [131] [132] [133] Overfull \hbox (0.72966pt too wide) in paragraph at lines 7093--7097 \OT1/ptm/m/n/10 If DoAniso-Pres-sureIM-Cou-pling is true, the in-for-ma-tion ex -changed be-tween GM and IM al-lows for pres-sure anisotropy. [134] [135] [136] [137] [138] [139] Overfull \hbox (4.24501pt too wide) in paragraph at lines 7564--7564 []\OT1/pcr/m/n/10 3 iDirGravity(0 - central, 1 - X, 2 - Y , 3 - Z direction)[] [140] Overfull \hbox (10.65999pt too wide) in paragraph at lines 7650--7654 []\OT1/ptm/m/n/10 For Type-R-e-sis-tiv-ity='Spitzer' the re-sis-tiv-ity is very low in space plasma. The only pa-ram-e-ter read is the CoulombLog- [141] [142] [143] [144] [145] [146] [147] [148] [149] Overfull \hbox (1.021pt too wide) in paragraph at lines 8376--8380 []\OT1/ptm/m/n/10 The ra-dial grid goes from the in-ner bound-ary at rMag-ne-to gram (typ-i-cally 1) to the source sur-face ra-dius rSourceSur- [150] Overfull \hbox (6.39069pt too wide) in paragraph at lines 8433--8438 []\OT1/ptm/m/n/10 After read-ing the har-mon-ics file, the B0NEW lookup ta-ble is gen-er-ated and saved into the "har-mon-ics[]bxyz[]new.out" [151] [152] Overfull \hbox (4.24501pt too wide) in paragraph at lines 8578--8578 []\OT1/pcr/m/n/10 7.5E4 LperpTimesSqrtBSi (read for alfvenwav edissipation only)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 8578--8578 []\OT1/pcr/m/n/10 0.04 Crefl (read for alfvenwav edissipation only)[] [153] [154] [155] [156] [157] [158] [159] [160] [161]) (./output.tex [162] Chapter 4. [163] Overfull \hbox (40.65233pt too wide) in paragraph at lines 78--81 []\OT1/ptm/m/n/10 We have de-vel-opped a tool that makes the con-ver-sion of th e restart files rather easy. The \OT1/pcr/m/n/10 Scripts/ConvertRestart.pl [164] [165] [166] [167] [168] [169] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0000.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0000.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0001.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0001.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0002.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0002.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0003.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0003.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0004.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0004.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100.S IO2_run1/x=0_mhd_1_n0 000100_2_pe0000.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0000.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0001.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0001.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0002.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0002.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0003.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0003.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0004.tec[] [170] [171]) [172] Chapter 5. (./visualization.tex LaTeX Warning: Reference `sec:julia' on page 173 undefined on input line 24. [173]) (./synopticSW.tex [174] Chapter 6. LaTeX Warning: Reference `section:potentialfield' on page 175 undefined on inpu t line 20. LaTeX Warning: Reference `section:semiempirical' on page 175 undefined on input line 22. LaTeX Warning: Reference `eq:grad' on page 175 undefined on input line 60. LaTeX Warning: Reference `eq:DivB' on page 175 undefined on input line 60. [175] [176] LaTeX Warning: Reference `eq:SphNorm' on page 177 undefined on input line 164. Underfull \hbox (badness 10000) in paragraph at lines 191--195 [177] [178] [179] Overfull \hbox (16.24501pt too wide) in paragraph at lines 406--406 []\OT1/pcr/m/n/10 Journal of Geophysical Research, VOL. 113, A03104, doi:10.102 9/2007JA012797, 2008[] ) [180] (./USERMANUAL.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on USERMANUAL.pdf (180 pages, 589830 bytes). Transcript written on USERMANUAL.log. makeindex USERMANUAL.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file USERMANUAL.idx...done (0 entries accepted, 0 rejected). Nothing written in USERMANUAL.ind. Transcript written in USERMANUAL.ilg. pdflatex USERMANUAL.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./USERMANUAL.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) (./USERMANUAL.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./USERMANUAL.toc (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [3]) (./introduction.tex [4] Chapter 1. Underfull \vbox (badness 5970) has occurred while \output is active [5]) [6] Chapter 2. (./quickstart.tex (../../README.md Overfull \hbox (47.44444pt too wide) in paragraph at lines 24--24 [][] Overfull \hbox (63.64442pt too wide) in paragraph at lines 26--26 [][] [7] Underfull \vbox (badness 10000) has occurred while \output is active [8] Underfull \vbox (badness 10000) has occurred while \output is active [9]) [10] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [11] [12] [13] [14] [15] [16] LaTeX Warning: Reference `section:idl_visualization' on page 17 undefined on in put line 526. LaTeX Warning: Reference `section:tecplot_visualization' on page 17 undefined o n input line 527. [17]) (./hardware_software.tex [18]) (./installation.tex [19] Overfull \hbox (4.24501pt too wide) in paragraph at lines 47--47 [] \OT1/pcr/m/n/10 ConvertRestart.pl Script to convert the endiannes s of restart files[] [20] [21] Underfull \vbox (badness 4686) has occurred while \output is active [22 <./proc _dims.pdf>] [23] [24]) (./runs.tex [25] Overfull \hbox (3.43063pt too wide) in paragraph at lines 41--48 \OT1/ptm/m/n/10 scrip-tion given in the PARAM.XML (or the PARAM.pl file on sys- tems which do not have the XML-PARSER::EasyTree [26]) [27] [28] Chapter 3. (./param.tex [29] [30] [31] [32] [33] [34] Underfull \vbox (badness 10000) has occurred while \output is active [35] [36]) (../../PARAM.xmltex Underfull \vbox (badness 4765) has occurred while \output is active [37] [38] [39] Overfull \hbox (59.77959pt too wide) in paragraph at lines 160--163 []\OT1/ptm/m/n/10 The Tol-er-ance pa-ram-e-ter sets if the it-er-a-tive so-lu-t ion Witer is close enough to W, abs(W-Witer).le.Tolerance*[abs(W)+abs(Witer)], [40] Overfull \hbox (4.24501pt too wide) in paragraph at lines 300--300 []\OT1/pcr/m/n/10 NEW NamePlanet (rest of parameters read f or unknown planet)[] [41] [42] [43] [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 679--686 [46] Overfull \hbox (4.24501pt too wide) in paragraph at lines 693--693 []\OT1/pcr/m/n/10 F DoDebugGhost (parameter for show_B LK in library.f90)[] [47] [48] [49] [50] [51] [52] [53] [54] [55] Overfull \hbox (3.87938pt too wide) in paragraph at lines 1411--1415 []\OT1/ptm/m/n/10 The #NEWRESTART com-mand sets the fol-low-ing global vari-abl es: DoRestart=.true. (read restart files), DoRestart- [56] Overfull \hbox (70.24501pt too wide) in paragraph at lines 1475--1475 [] \OT1/pcr/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1475--1475 [] \OT1/pcr/m/n/10 radiative outflow boundaries are applied for radiation energy densities[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 outflow - same as 'float' but the pressure is set to pO utflow from #OUTFLOWPRESSURE[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 reflect - reflective (anti-symmetric for the normal com ponents of V and B,[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 linetied - symmetric for density, anti-symmetric for mom entum, float all others[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 inflow/vary - time dependent boundary based on solar wind i nput file (#SOLARWINDFILE)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 ihbuffer - values obtained from the IH component (this i s set automatically)[] Overfull \hbox (82.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 none - do not change ghost cells. This is useful if the outer boundary is not used.[] [57] Overfull \hbox (8.74103pt too wide) in paragraph at lines 1529--1535 []\OT1/ptm/m/n/10 The outer bound-aries have to be face based if a brick-shaped com-pu-ta-tional do-main is cut out from the sphere/cylinder Overfull \hbox (70.24501pt too wide) in paragraph at lines 1551--1551 [] \OT1/pcr/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1551--1551 [] \OT1/pcr/m/n/10 radiative outflow boundaries are applied for radiation energy densities[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 outflow - same as 'float' but the pressure is set to pO utflow from #OUTFLOWPRESSURE[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflect - reflect the normal component of B1, reflect t he full velocity vector[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflectb - reflect the normal component of full B, refle ct the full velocity vector[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflectall - reflect the normal component of B1 and veloci ty, symmetric for all other[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 fixed - fixed values (set by #SOLARWIND or #BOUNDARYS TATE), total B is set[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 inflow/vary - time dependent boundary based on solar wind i nput file (#SOLARWINDFILE)[] [58] [59] Overfull \hbox (40.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'reflectb' - same as reflect, but the normal component of full B is reflected.[] Overfull \hbox (88.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'outflow' - same as 'float' but the pressure is set t o pOutflow from #OUTFLOWPRESSURE[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'fixed' - use initial solar wind values. Total B is set to solar wind B.[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'fixedb1' - use initial solar wind values. B1 is set is to solar wind B.[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'ionosphere' - reflect velocity relative to corotation + ionosphere ExB drift[] Overfull \hbox (136.24501pt too wide) in paragraph at lines 1697--1697 [] \OT1/pcr/m/n/10 is applied above 55 degrees latitude. Se e #OUTFLOWCRITERIA for more information.[] [60] [61] [62] [63] [64] [65] Overfull \hbox (68.17989pt too wide) in paragraph at lines 2103--2106 \OT1/ptm/m/n/10 TypeCoordSystem de-fines the co-or-di-nate sys-tem for the com- po-nent. The co-or-di-nate sys-tems are de-fined in share/Library/src/CON[]axes . [66] [67] [68] [69] Overfull \hbox (0.18028pt too wide) in paragraph at lines 2491--2493 []\OT1/ptm/m/n/10 If the #SCHEME com-mand is not used, then the de-faults are n Stage=2 with the half-step pre-dic-tor and CflExpl=0.8. [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 2777--2780 Overfull \hbox (6.39099pt too wide) in paragraph at lines 2822--2827 []\OT1/ptm/m/n/10 For steady state run the de-fault is the back-ward Eu-ler sch eme, which cor-re-sponds to Im-plCo-eff=1.0 and UsedBdf2=F. [74] [75] Overfull \hbox (4.24501pt too wide) in paragraph at lines 2971--2971 []\OT1/pcr/m/n/10 MBILU TypePrecond (MBILU, BILU, DILU, GS, BLOCKJACO BI, JACOBI, HYPRE)[] [76] [77] [78] [79] Overfull \hbox (73.71059pt too wide) in paragraph at lines 3226--3233 \OT1/ptm/m/n/10 saved only at the end. A bi-nary restart file is pro-duced for ev-ery block and named as RESTARTOUT-DIR/blkGLOBALBLKNUMBER.rst. Overfull \hbox (1.97142pt too wide) in paragraph at lines 3234--3237 []\OT1/ptm/m/n/10 The restart files are over-writ-ten ev-ery time a new restart is done, but one can change the name of the RESTARTOUT- [80] Overfull \hbox (4.48077pt too wide) in paragraph at lines 3290--3293 []\OT1/ptm/m/n/10 The pos-si-ble val-ues for StringLog-Var and the cor-re-spond -ing vari-ables to-gether with the de-fault val-ues for StringLog- Overfull \hbox (46.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 VAR - average of variable VAR (listed in Name Var_V of ModEquation.f90)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Erad Ew - average radiation/wave energy (summed f or all groups/waves)[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Lon1 Lon2 Status - average of longitude and status of fiel dline (for testing)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 VARpnt - point value of VAR (listed in NameVar_V ) at the test cell[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Statuspnt - point value of status of fieldline trac ing from test cell:[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Jinmax Joutmax - maximum of inward and outward currents at rCurrents of #BODY[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Jin Jout - surface integral of inward and outward currents at rCurrents[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Aflx - surface integral of 1 at radii def ined in rLog (area)[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Pvecflx - surface integral of ExB at radii def ined in rLog (Poynting flux)[] Overfull \hbox (40.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Dstflx - surface integral of B1z at radii def ined in rLog (Dst index)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 DstDivb - error of the dstflx integral due to fin ite value of div B[] [81] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3357--3357 [] \OT1/pcr/m/n/10 none - there will be no indication of time in the logfile ( not even the number of steps)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 3357--3357 [] \OT1/pcr/m/n/10 date - date-time as 7 integers: year month day hour minute second millisecond,[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 2011-02-01T00:00:00 UT StringStartTimeTraj ! Read if StringS atellite contains 'trajrange'[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 2011-02-10T00:00:00 UT StringEndTimeTraj ! Read if StringS atellite contains 'trajrange'[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 1 h StringDtTraj ! Read if StringS atellite contains 'trajrange'[] [82] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3460--3460 [] \OT1/pcr/m/n/10 date - date-time as 7 integers: year month day hour minute second millisecond[] [83] Overfull \hbox (28.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 'YYYY MM DD HH MM SS MSC UT' (single digit need t o fill 0 ahead and the[] Overfull \hbox (40.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 sperator ('-', ':', 'T', ' ') between numbers can be whatever characters)[] Overfull \hbox (76.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 Any number followed by ' w'/' d'/' h'/' m'/' s', in which ca se the time is with respect to[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 #STARTTIME. For example, 1 h here means StartTime + 1 hour. THERE IS A SPACE[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 Any number (in which case it is assumed to be in seconds), i n which case the time[] [84] [85] [86] [87] [88] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 1d HD idl_tec StringPlot ! 1d plot (with Tecplot he ader) along X axis[] Underfull \vbox (badness 10000) has occurred while \output is active [89] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 eqr eqr idl StringPlot ! Equatorial (magnetic) fi eld line tracing info[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 20 nRadius ! Starting points on the S M equatorial plane[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 20 nRadius ! Starting points on the S M equatorial plane[] Underfull \vbox (badness 10000) has occurred while \output is active [90] Overfull \hbox (10.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 lcb int tec StringPlot !last closed field line p lots with integrals[] Underfull \vbox (badness 10000) has occurred while \output is active [91] Underfull \vbox (badness 10000) has occurred while \output is active [92] Underfull \vbox (badness 10000) has occurred while \output is active [93] [94] Overfull \hbox (34.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'ray' - vars: bx by bz lon1 lat1 lon2 lat2 status blk (if DoMapEquatorRay=F)[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 vars: bx by bz req1 phi1 req2 phi2 status blk (if DoMapEquatorRay=T)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'eqr' - vars: iLine l x y z rho ux uy uz bx by bz p rCurve (for all rays traced)[] Overfull \hbox (82.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'eqb' - vars: z PrimVarMinB rCurve xZ0 yZ0 zZ0 PrimVarZ0 rCu rveZ0 (B is in SM coordinates)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'pos' - vars x y z (PlotArea='lin' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'sol' - vars: wl pb (PlotArea='los' only)[] Overfull \hbox (94.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'lgq' - vars: squash.03 squash.12 squash.2 squash-15 squash- 2 squash-3 (PlotArea='los' only)[] [95] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'euv' - vars: euv171 euv195 euv284 (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'sxr' - vars: sxr (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'tbl' - vars: listed in the LOS table file (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'dem' - vars: DEM, EM (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'int' - vars: 1/B n/B p/B (PlotArea='lcb' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'nul' - vars: (PlotArea='lcb' only)[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'ins' - vars: determined by the corresponding instrument, se e line-of-sight below[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 - pars: determined by the corresponding instrument, se e line-of-sight below[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 RadiusMin RadiusMax if PlotArea is 'eqr', 'eqb', 'shl', 'sln', 'slg', 'shk'[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 dRadius, dLon, dLat if PlotArea is 'sln', 'slg' or 'shl' and range is nonzero.[] Overfull \hbox (160.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 DxSavePlot if PlotForm is 'idl' and PlotArea is not box/shl/sln/slg/shk/los/rfr/lin/eqr/eqb[] [96] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4372--4372 [] \OT1/pcr/m/n/10 HGI coordinates (SC,IH and OH) or the GM coordinates[] [97] Underfull \hbox (badness 10000) in paragraph at lines 4432--4441 [98] [99] [100] [101] [102] Overfull \hbox (7.63066pt too wide) in paragraph at lines 4767--4773 []\OT1/ptm/m/n/10 The lat-est im-ple-men-ta-tion for the Gibson-Low erup-tive e vent gen-er-a-tor (Type-Cme=GL) fol-lows the pa-per Borovikov, [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] Overfull \hbox (4.24501pt too wide) in paragraph at lines 5679--5679 [] \OT1/pcr/m/n/10 'transient RhoU_dot' - relative change of momentum ( d|rhoU|/dt)/|rhoU|[] [115] [116] Overfull \hbox (2.72028pt too wide) in paragraph at lines 5831--5836 \OT1/ptm/m/n/10 This com-mand is only use-ful if the nOrder is larger than 2 in the #SCHEME com-mand. In this case the StringLowOrder- [117] [118] [119] [120] [121] [122] Overfull \hbox (11.43059pt too wide) in paragraph at lines 6255--6258 []\OT1/ptm/m/n/10 When Us-eSin-gleIon-Ve-loc-ity is true, the ion ve-loc-i-ties are set to the av-er-age fluid ve-loc-ity $\OML/cmm/m/it/10 u \OT1/cmr/m/n/10 = [] []\OML/cmm/m/it/10 s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]su[]s\OT1/cmr/m /n/10 )\OML/cmm/m/it/10 = [] []s^^Z[]s$ Overfull \hbox (65.49863pt too wide) in paragraph at lines 6259--6262 []\OT1/ptm/m/n/10 When Us-eSin-gleIon-Tem-per-a-ture is true, the ion tem-per-a -tures are set to the av-er-age tem-per-a-ture $\OML/cmm/m/it/10 k[]BT \OT1/cmr /m/n/10 = [] []\OML/cmm/m/it/10 sp[]s= [] []s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]s=M[]s\OT1/cmr/m/n/10 )$ Overfull \hbox (4.24501pt too wide) in paragraph at lines 6273--6273 []\OT1/pcr/m/n/10 100.0 uCutOffDim [km/s] read if Tau CutOffDim positive[] [123] Overfull \hbox (61.65004pt too wide) in paragraph at lines 6295--6303 \OT1/ptm/m/n/10 comes large. Set-ting uCut-offDim = -1.0 switches to a physics based cut-off ve-loc-ity which is de-fined as B/sqrt[rho1*rho2/(rho1+rho2)] [124] [125] [126] [127] [128] Overfull \hbox (4.24501pt too wide) in paragraph at lines 6751--6751 []\OT1/pcr/m/n/10 cg TypeProjectIter:'cg' or 'bicgstab' fo r iterative scheme[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 6751--6751 []\OT1/pcr/m/n/10 rel TypeProjectStop:'rel' or 'max' error for stop condition[] [129] [130] [131] [132] [133] Overfull \hbox (0.72966pt too wide) in paragraph at lines 7093--7097 \OT1/ptm/m/n/10 If DoAniso-Pres-sureIM-Cou-pling is true, the in-for-ma-tion ex -changed be-tween GM and IM al-lows for pres-sure anisotropy. [134] [135] [136] [137] [138] [139] Overfull \hbox (4.24501pt too wide) in paragraph at lines 7564--7564 []\OT1/pcr/m/n/10 3 iDirGravity(0 - central, 1 - X, 2 - Y , 3 - Z direction)[] [140] Overfull \hbox (10.65999pt too wide) in paragraph at lines 7650--7654 []\OT1/ptm/m/n/10 For Type-R-e-sis-tiv-ity='Spitzer' the re-sis-tiv-ity is very low in space plasma. The only pa-ram-e-ter read is the CoulombLog- [141] [142] [143] [144] [145] [146] [147] [148] [149] Overfull \hbox (1.021pt too wide) in paragraph at lines 8376--8380 []\OT1/ptm/m/n/10 The ra-dial grid goes from the in-ner bound-ary at rMag-ne-to gram (typ-i-cally 1) to the source sur-face ra-dius rSourceSur- [150] Overfull \hbox (6.39069pt too wide) in paragraph at lines 8433--8438 []\OT1/ptm/m/n/10 After read-ing the har-mon-ics file, the B0NEW lookup ta-ble is gen-er-ated and saved into the "har-mon-ics[]bxyz[]new.out" [151] [152] Overfull \hbox (4.24501pt too wide) in paragraph at lines 8578--8578 []\OT1/pcr/m/n/10 7.5E4 LperpTimesSqrtBSi (read for alfvenwav edissipation only)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 8578--8578 []\OT1/pcr/m/n/10 0.04 Crefl (read for alfvenwav edissipation only)[] [153] [154] [155] [156] [157] [158] [159] [160] [161]) (./output.tex [162] Chapter 4. [163] Overfull \hbox (40.65233pt too wide) in paragraph at lines 78--81 []\OT1/ptm/m/n/10 We have de-vel-opped a tool that makes the con-ver-sion of th e restart files rather easy. The \OT1/pcr/m/n/10 Scripts/ConvertRestart.pl [164] [165] [166] [167] [168] [169] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0000.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0000.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0001.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0001.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0002.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0002.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0003.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0003.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0004.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0004.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100.S IO2_run1/x=0_mhd_1_n0 000100_2_pe0000.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0000.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0001.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0001.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0002.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0002.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0003.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0003.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0004.tec[] [170] [171]) [172] Chapter 5. (./visualization.tex LaTeX Warning: Reference `sec:julia' on page 173 undefined on input line 24. [173]) (./synopticSW.tex [174] Chapter 6. [175] [176] Underfull \hbox (badness 10000) in paragraph at lines 191--195 [177] [178] [179] Overfull \hbox (16.24501pt too wide) in paragraph at lines 406--406 []\OT1/pcr/m/n/10 Journal of Geophysical Research, VOL. 113, A03104, doi:10.102 9/2007JA012797, 2008[] ) [180] (./USERMANUAL.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on USERMANUAL.pdf (180 pages, 592254 bytes). Transcript written on USERMANUAL.log. makeindex USERMANUAL.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file USERMANUAL.idx...done (0 entries accepted, 0 rejected). Nothing written in USERMANUAL.ind. Transcript written in USERMANUAL.ilg. pdflatex USERMANUAL.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./USERMANUAL.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./sverb.sty) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) (./USERMANUAL.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./USERMANUAL.toc (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [3]) (./introduction.tex [4] Chapter 1. Underfull \vbox (badness 5970) has occurred while \output is active [5]) [6] Chapter 2. (./quickstart.tex (../../README.md Overfull \hbox (47.44444pt too wide) in paragraph at lines 24--24 [][] Overfull \hbox (63.64442pt too wide) in paragraph at lines 26--26 [][] [7] Underfull \vbox (badness 10000) has occurred while \output is active [8] Underfull \vbox (badness 10000) has occurred while \output is active [9]) [10] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [11] [12] [13] [14] [15] [16] LaTeX Warning: Reference `section:idl_visualization' on page 17 undefined on in put line 526. LaTeX Warning: Reference `section:tecplot_visualization' on page 17 undefined o n input line 527. [17]) (./hardware_software.tex [18]) (./installation.tex [19] Overfull \hbox (4.24501pt too wide) in paragraph at lines 47--47 [] \OT1/pcr/m/n/10 ConvertRestart.pl Script to convert the endiannes s of restart files[] [20] [21] Underfull \vbox (badness 4686) has occurred while \output is active [22 <./proc _dims.pdf>] [23] [24]) (./runs.tex [25] Overfull \hbox (3.43063pt too wide) in paragraph at lines 41--48 \OT1/ptm/m/n/10 scrip-tion given in the PARAM.XML (or the PARAM.pl file on sys- tems which do not have the XML-PARSER::EasyTree [26]) [27] [28] Chapter 3. (./param.tex [29] [30] [31] [32] [33] [34] Underfull \vbox (badness 10000) has occurred while \output is active [35] [36]) (../../PARAM.xmltex Underfull \vbox (badness 4765) has occurred while \output is active [37] [38] [39] Overfull \hbox (59.77959pt too wide) in paragraph at lines 160--163 []\OT1/ptm/m/n/10 The Tol-er-ance pa-ram-e-ter sets if the it-er-a-tive so-lu-t ion Witer is close enough to W, abs(W-Witer).le.Tolerance*[abs(W)+abs(Witer)], [40] Overfull \hbox (4.24501pt too wide) in paragraph at lines 300--300 []\OT1/pcr/m/n/10 NEW NamePlanet (rest of parameters read f or unknown planet)[] [41] [42] [43] [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 679--686 [46] Overfull \hbox (4.24501pt too wide) in paragraph at lines 693--693 []\OT1/pcr/m/n/10 F DoDebugGhost (parameter for show_B LK in library.f90)[] [47] [48] [49] [50] [51] [52] [53] [54] [55] Overfull \hbox (3.87938pt too wide) in paragraph at lines 1411--1415 []\OT1/ptm/m/n/10 The #NEWRESTART com-mand sets the fol-low-ing global vari-abl es: DoRestart=.true. (read restart files), DoRestart- [56] Overfull \hbox (70.24501pt too wide) in paragraph at lines 1475--1475 [] \OT1/pcr/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1475--1475 [] \OT1/pcr/m/n/10 radiative outflow boundaries are applied for radiation energy densities[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 outflow - same as 'float' but the pressure is set to pO utflow from #OUTFLOWPRESSURE[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 reflect - reflective (anti-symmetric for the normal com ponents of V and B,[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 linetied - symmetric for density, anti-symmetric for mom entum, float all others[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 inflow/vary - time dependent boundary based on solar wind i nput file (#SOLARWINDFILE)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 ihbuffer - values obtained from the IH component (this i s set automatically)[] Overfull \hbox (82.24501pt too wide) in paragraph at lines 1475--1475 []\OT1/pcr/m/n/10 none - do not change ghost cells. This is useful if the outer boundary is not used.[] [57] Overfull \hbox (8.74103pt too wide) in paragraph at lines 1529--1535 []\OT1/ptm/m/n/10 The outer bound-aries have to be face based if a brick-shaped com-pu-ta-tional do-main is cut out from the sphere/cylinder Overfull \hbox (70.24501pt too wide) in paragraph at lines 1551--1551 [] \OT1/pcr/m/n/10 Phi=0 set for the scalar in hyperbolic div B control (see #HYPERBOLICDIVB)[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1551--1551 [] \OT1/pcr/m/n/10 radiative outflow boundaries are applied for radiation energy densities[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 outflow - same as 'float' but the pressure is set to pO utflow from #OUTFLOWPRESSURE[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflect - reflect the normal component of B1, reflect t he full velocity vector[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflectb - reflect the normal component of full B, refle ct the full velocity vector[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 reflectall - reflect the normal component of B1 and veloci ty, symmetric for all other[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 fixed - fixed values (set by #SOLARWIND or #BOUNDARYS TATE), total B is set[] Overfull \hbox (52.24501pt too wide) in paragraph at lines 1551--1551 []\OT1/pcr/m/n/10 inflow/vary - time dependent boundary based on solar wind i nput file (#SOLARWINDFILE)[] [58] [59] Overfull \hbox (40.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'reflectb' - same as reflect, but the normal component of full B is reflected.[] Overfull \hbox (88.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'outflow' - same as 'float' but the pressure is set t o pOutflow from #OUTFLOWPRESSURE[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'fixed' - use initial solar wind values. Total B is set to solar wind B.[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'fixedb1' - use initial solar wind values. B1 is set is to solar wind B.[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 1697--1697 []\OT1/pcr/m/n/10 'ionosphere' - reflect velocity relative to corotation + ionosphere ExB drift[] Overfull \hbox (136.24501pt too wide) in paragraph at lines 1697--1697 [] \OT1/pcr/m/n/10 is applied above 55 degrees latitude. Se e #OUTFLOWCRITERIA for more information.[] [60] [61] [62] [63] [64] [65] Overfull \hbox (68.17989pt too wide) in paragraph at lines 2103--2106 \OT1/ptm/m/n/10 TypeCoordSystem de-fines the co-or-di-nate sys-tem for the com- po-nent. The co-or-di-nate sys-tems are de-fined in share/Library/src/CON[]axes . [66] [67] [68] [69] Overfull \hbox (0.18028pt too wide) in paragraph at lines 2491--2493 []\OT1/ptm/m/n/10 If the #SCHEME com-mand is not used, then the de-faults are n Stage=2 with the half-step pre-dic-tor and CflExpl=0.8. [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 2777--2780 Overfull \hbox (6.39099pt too wide) in paragraph at lines 2822--2827 []\OT1/ptm/m/n/10 For steady state run the de-fault is the back-ward Eu-ler sch eme, which cor-re-sponds to Im-plCo-eff=1.0 and UsedBdf2=F. [74] [75] Overfull \hbox (4.24501pt too wide) in paragraph at lines 2971--2971 []\OT1/pcr/m/n/10 MBILU TypePrecond (MBILU, BILU, DILU, GS, BLOCKJACO BI, JACOBI, HYPRE)[] [76] [77] [78] [79] Overfull \hbox (73.71059pt too wide) in paragraph at lines 3226--3233 \OT1/ptm/m/n/10 saved only at the end. A bi-nary restart file is pro-duced for ev-ery block and named as RESTARTOUT-DIR/blkGLOBALBLKNUMBER.rst. Overfull \hbox (1.97142pt too wide) in paragraph at lines 3234--3237 []\OT1/ptm/m/n/10 The restart files are over-writ-ten ev-ery time a new restart is done, but one can change the name of the RESTARTOUT- [80] Overfull \hbox (4.48077pt too wide) in paragraph at lines 3290--3293 []\OT1/ptm/m/n/10 The pos-si-ble val-ues for StringLog-Var and the cor-re-spond -ing vari-ables to-gether with the de-fault val-ues for StringLog- Overfull \hbox (46.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 VAR - average of variable VAR (listed in Name Var_V of ModEquation.f90)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Erad Ew - average radiation/wave energy (summed f or all groups/waves)[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Lon1 Lon2 Status - average of longitude and status of fiel dline (for testing)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 VARpnt - point value of VAR (listed in NameVar_V ) at the test cell[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Statuspnt - point value of status of fieldline trac ing from test cell:[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Jinmax Joutmax - maximum of inward and outward currents at rCurrents of #BODY[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Jin Jout - surface integral of inward and outward currents at rCurrents[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Aflx - surface integral of 1 at radii def ined in rLog (area)[] Overfull \hbox (64.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Pvecflx - surface integral of ExB at radii def ined in rLog (Poynting flux)[] Overfull \hbox (40.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 Dstflx - surface integral of B1z at radii def ined in rLog (Dst index)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 3350--3350 []\OT1/pcr/m/n/10 DstDivb - error of the dstflx integral due to fin ite value of div B[] [81] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3357--3357 [] \OT1/pcr/m/n/10 none - there will be no indication of time in the logfile ( not even the number of steps)[] Overfull \hbox (16.24501pt too wide) in paragraph at lines 3357--3357 [] \OT1/pcr/m/n/10 date - date-time as 7 integers: year month day hour minute second millisecond,[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 2011-02-01T00:00:00 UT StringStartTimeTraj ! Read if StringS atellite contains 'trajrange'[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 2011-02-10T00:00:00 UT StringEndTimeTraj ! Read if StringS atellite contains 'trajrange'[] Overfull \hbox (70.24501pt too wide) in paragraph at lines 3400--3400 []\OT1/pcr/m/n/10 1 h StringDtTraj ! Read if StringS atellite contains 'trajrange'[] [82] Overfull \hbox (10.24501pt too wide) in paragraph at lines 3460--3460 [] \OT1/pcr/m/n/10 date - date-time as 7 integers: year month day hour minute second millisecond[] [83] Overfull \hbox (28.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 'YYYY MM DD HH MM SS MSC UT' (single digit need t o fill 0 ahead and the[] Overfull \hbox (40.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 sperator ('-', ':', 'T', ' ') between numbers can be whatever characters)[] Overfull \hbox (76.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 Any number followed by ' w'/' d'/' h'/' m'/' s', in which ca se the time is with respect to[] Overfull \hbox (58.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 #STARTTIME. For example, 1 h here means StartTime + 1 hour. THERE IS A SPACE[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 3527--3527 [] \OT1/pcr/m/n/10 Any number (in which case it is assumed to be in seconds), i n which case the time[] [84] [85] [86] [87] [88] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 1d HD idl_tec StringPlot ! 1d plot (with Tecplot he ader) along X axis[] Underfull \vbox (badness 10000) has occurred while \output is active [89] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 eqr eqr idl StringPlot ! Equatorial (magnetic) fi eld line tracing info[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 20 nRadius ! Starting points on the S M equatorial plane[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 20 nRadius ! Starting points on the S M equatorial plane[] Underfull \vbox (badness 10000) has occurred while \output is active [90] Overfull \hbox (10.24501pt too wide) in paragraph at lines 4117--4117 []\OT1/pcr/m/n/10 lcb int tec StringPlot !last closed field line p lots with integrals[] Underfull \vbox (badness 10000) has occurred while \output is active [91] Underfull \vbox (badness 10000) has occurred while \output is active [92] Underfull \vbox (badness 10000) has occurred while \output is active [93] [94] Overfull \hbox (34.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'ray' - vars: bx by bz lon1 lat1 lon2 lat2 status blk (if DoMapEquatorRay=F)[] Overfull \hbox (34.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 vars: bx by bz req1 phi1 req2 phi2 status blk (if DoMapEquatorRay=T)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'eqr' - vars: iLine l x y z rho ux uy uz bx by bz p rCurve (for all rays traced)[] Overfull \hbox (82.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'eqb' - vars: z PrimVarMinB rCurve xZ0 yZ0 zZ0 PrimVarZ0 rCu rveZ0 (B is in SM coordinates)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'pos' - vars x y z (PlotArea='lin' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'sol' - vars: wl pb (PlotArea='los' only)[] Overfull \hbox (94.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'lgq' - vars: squash.03 squash.12 squash.2 squash-15 squash- 2 squash-3 (PlotArea='los' only)[] [95] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'euv' - vars: euv171 euv195 euv284 (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'sxr' - vars: sxr (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'tbl' - vars: listed in the LOS table file (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'dem' - vars: DEM, EM (PlotArea='los' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'int' - vars: 1/B n/B p/B (PlotArea='lcb' only)[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'nul' - vars: (PlotArea='lcb' only)[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 'ins' - vars: determined by the corresponding instrument, se e line-of-sight below[] Overfull \hbox (22.24501pt too wide) in paragraph at lines 4254--4254 [] \OT1/pcr/m/n/10 - pars: determined by the corresponding instrument, se e line-of-sight below[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 RadiusMin RadiusMax if PlotArea is 'eqr', 'eqb', 'shl', 'sln', 'slg', 'shk'[] Overfull \hbox (28.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 dRadius, dLon, dLat if PlotArea is 'sln', 'slg' or 'shl' and range is nonzero.[] Overfull \hbox (160.24501pt too wide) in paragraph at lines 4277--4277 [] \OT1/pcr/m/n/10 DxSavePlot if PlotForm is 'idl' and PlotArea is not box/shl/sln/slg/shk/los/rfr/lin/eqr/eqb[] [96] Overfull \hbox (4.24501pt too wide) in paragraph at lines 4372--4372 [] \OT1/pcr/m/n/10 HGI coordinates (SC,IH and OH) or the GM coordinates[] [97] Underfull \hbox (badness 10000) in paragraph at lines 4432--4441 [98] [99] [100] [101] [102] Overfull \hbox (7.63066pt too wide) in paragraph at lines 4767--4773 []\OT1/ptm/m/n/10 The lat-est im-ple-men-ta-tion for the Gibson-Low erup-tive e vent gen-er-a-tor (Type-Cme=GL) fol-lows the pa-per Borovikov, [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] Overfull \hbox (4.24501pt too wide) in paragraph at lines 5679--5679 [] \OT1/pcr/m/n/10 'transient RhoU_dot' - relative change of momentum ( d|rhoU|/dt)/|rhoU|[] [115] [116] Overfull \hbox (2.72028pt too wide) in paragraph at lines 5831--5836 \OT1/ptm/m/n/10 This com-mand is only use-ful if the nOrder is larger than 2 in the #SCHEME com-mand. In this case the StringLowOrder- [117] [118] [119] [120] [121] [122] Overfull \hbox (11.43059pt too wide) in paragraph at lines 6255--6258 []\OT1/ptm/m/n/10 When Us-eSin-gleIon-Ve-loc-ity is true, the ion ve-loc-i-ties are set to the av-er-age fluid ve-loc-ity $\OML/cmm/m/it/10 u \OT1/cmr/m/n/10 = [] []\OML/cmm/m/it/10 s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]su[]s\OT1/cmr/m /n/10 )\OML/cmm/m/it/10 = [] []s^^Z[]s$ Overfull \hbox (65.49863pt too wide) in paragraph at lines 6259--6262 []\OT1/ptm/m/n/10 When Us-eSin-gleIon-Tem-per-a-ture is true, the ion tem-per-a -tures are set to the av-er-age tem-per-a-ture $\OML/cmm/m/it/10 k[]BT \OT1/cmr /m/n/10 = [] []\OML/cmm/m/it/10 sp[]s= [] []s\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^Z[]s=M[]s\OT1/cmr/m/n/10 )$ Overfull \hbox (4.24501pt too wide) in paragraph at lines 6273--6273 []\OT1/pcr/m/n/10 100.0 uCutOffDim [km/s] read if Tau CutOffDim positive[] [123] Overfull \hbox (61.65004pt too wide) in paragraph at lines 6295--6303 \OT1/ptm/m/n/10 comes large. Set-ting uCut-offDim = -1.0 switches to a physics based cut-off ve-loc-ity which is de-fined as B/sqrt[rho1*rho2/(rho1+rho2)] [124] [125] [126] [127] [128] Overfull \hbox (4.24501pt too wide) in paragraph at lines 6751--6751 []\OT1/pcr/m/n/10 cg TypeProjectIter:'cg' or 'bicgstab' fo r iterative scheme[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 6751--6751 []\OT1/pcr/m/n/10 rel TypeProjectStop:'rel' or 'max' error for stop condition[] [129] [130] [131] [132] [133] Overfull \hbox (0.72966pt too wide) in paragraph at lines 7093--7097 \OT1/ptm/m/n/10 If DoAniso-Pres-sureIM-Cou-pling is true, the in-for-ma-tion ex -changed be-tween GM and IM al-lows for pres-sure anisotropy. [134] [135] [136] [137] [138] [139] Overfull \hbox (4.24501pt too wide) in paragraph at lines 7564--7564 []\OT1/pcr/m/n/10 3 iDirGravity(0 - central, 1 - X, 2 - Y , 3 - Z direction)[] [140] Overfull \hbox (10.65999pt too wide) in paragraph at lines 7650--7654 []\OT1/ptm/m/n/10 For Type-R-e-sis-tiv-ity='Spitzer' the re-sis-tiv-ity is very low in space plasma. The only pa-ram-e-ter read is the CoulombLog- [141] [142] [143] [144] [145] [146] [147] [148] [149] Overfull \hbox (1.021pt too wide) in paragraph at lines 8376--8380 []\OT1/ptm/m/n/10 The ra-dial grid goes from the in-ner bound-ary at rMag-ne-to gram (typ-i-cally 1) to the source sur-face ra-dius rSourceSur- [150] Overfull \hbox (6.39069pt too wide) in paragraph at lines 8433--8438 []\OT1/ptm/m/n/10 After read-ing the har-mon-ics file, the B0NEW lookup ta-ble is gen-er-ated and saved into the "har-mon-ics[]bxyz[]new.out" [151] [152] Overfull \hbox (4.24501pt too wide) in paragraph at lines 8578--8578 []\OT1/pcr/m/n/10 7.5E4 LperpTimesSqrtBSi (read for alfvenwav edissipation only)[] Overfull \hbox (4.24501pt too wide) in paragraph at lines 8578--8578 []\OT1/pcr/m/n/10 0.04 Crefl (read for alfvenwav edissipation only)[] [153] [154] [155] [156] [157] [158] [159] [160] [161]) (./output.tex [162] Chapter 4. [163] Overfull \hbox (40.65233pt too wide) in paragraph at lines 78--81 []\OT1/ptm/m/n/10 We have de-vel-opped a tool that makes the con-ver-sion of th e restart files rather easy. The \OT1/pcr/m/n/10 Scripts/ConvertRestart.pl [164] [165] [166] [167] [168] [169] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0000.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0000.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0001.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0001.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0002.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0002.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0003.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0003.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spN_mhd_2_n0000100_pe0004.tec IO2_run1/x=0_mhd_1_n0 000100_1_pe0004.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100.S IO2_run1/x=0_mhd_1_n0 000100_2_pe0000.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0000.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0001.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0001.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0002.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0002.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0003.tec[] Overfull \hbox (10.24501pt too wide) in paragraph at lines 567--567 []\OT1/pcr/m/n/10 IO2_run1/spS_mhd_2_n0000100_pe0003.tec IO2_run1/x=0_mhd_1_n0 000100_2_pe0004.tec[] [170] [171]) [172] Chapter 5. (./visualization.tex LaTeX Warning: Reference `sec:julia' on page 173 undefined on input line 24. [173]) (./synopticSW.tex [174] Chapter 6. [175] [176] Underfull \hbox (badness 10000) in paragraph at lines 191--195 [177] [178] [179] Overfull \hbox (16.24501pt too wide) in paragraph at lines 406--406 []\OT1/pcr/m/n/10 Journal of Geophysical Research, VOL. 113, A03104, doi:10.102 9/2007JA012797, 2008[] ) [180] (./USERMANUAL.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on USERMANUAL.pdf (180 pages, 592254 bytes). Transcript written on USERMANUAL.log. mv USERMANUAL.pdf ../ rm -f USERMANUAL.ind USERMANUAL.idx USERMANUAL.ilg touch DESIGN.ind DESIGN.idx pdflatex DESIGN.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./DESIGN.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) No file DESIGN.aux. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] No file DESIGN.toc. [3] [4] Chapter 1. (./grid.tex LaTeX Warning: Reference `fig:blocks' on page 5 undefined on input line 52. LaTeX Warning: Reference `fig:refine_coarsen' on page 5 undefined on input line 55. LaTeX Warning: Reference `fig:blocks' on page 5 undefined on input line 86. LaTeX Warning: Reference `fig:blocks' on page 5 undefined on input line 87. LaTeX Warning: Reference `fig:blocks' on page 5 undefined on input line 96. LaTeX Warning: Reference `fig:message_pass_equal' on page 5 undefined on input line 96. LaTeX Warning: Reference `fig:message_pass_res_change' on page 5 undefined on i nput line 97. LaTeX Warning: Reference `fig:message_pass_equal' on page 5 undefined on input line 99. LaTeX Warning: Reference `fig:message_pass_res_change' on page 5 undefined on i nput line 102. LaTeX Warning: Reference `section:finite_volume' on page 5 undefined on input l ine 110. [5] [6 <./adaptiveblock.pdf> <./adapted_grid.pdf>] [7 <./message_pass_equal.pdf > <./message_pass_res_change.pdf>] LaTeX Warning: Reference `fig:refine_coarsen' on page 8 undefined on input line 156. ) (./temporal.tex LaTeX Warning: Reference `eq:continuity_conserve' on page 8 undefined on input line 16. LaTeX Warning: Reference `eq:energy_conserve' on page 8 undefined on input line 16. LaTeX Warning: Reference `q-local' on page 8 undefined on input line 43. LaTeX Warning: Reference `q-local' on page 8 undefined on input line 46. LaTeX Warning: Reference `q-compact' on page 8 undefined on input line 47. [8] LaTeX Warning: Reference `q-local-dt' on page 9 undefined on input line 83. LaTeX Warning: Reference `q-one-stage' on page 9 undefined on input line 88. LaTeX Warning: Reference `q-one-stage' on page 9 undefined on input line 102. LaTeX Warning: Reference `q-one-stage' on page 9 undefined on input line 123. [9]) (./spatial.tex LaTeX Warning: Reference `fig:fivol' on page 10 undefined on input line 48. LaTeX Warning: Reference `q-compact' on page 10 undefined on input line 49. [10 <./fivol.pdf>] LaTeX Warning: Reference `q-two-stage' on page 11 undefined on input line 68. LaTeX Warning: Reference `q-roe' on page 11 undefined on input line 138. [11] LaTeX Warning: Reference `q-roe' on page 12 undefined on input line 144. LaTeX Warning: Reference `q-local-dt' on page 12 undefined on input line 152. [12] LaTeX Warning: Reference `fig:limiter' on page 13 undefined on input line 230. ) (./divb.tex LaTeX Warning: Reference `eq:momentum_conserve' on page 13 undefined on input l ine 34. LaTeX Warning: Reference `eq:energy_conserve' on page 13 undefined on input lin e 34. LaTeX Warning: Reference `eq:bfield_conserve' on page 13 undefined on input lin e 35. [13 <./slope.pdf>] [14] LaTeX Warning: Reference `q-inductiondiff' on page 15 undefined on input line 1 18. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [15]) [16] (./DESIGN.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ){/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on DESIGN.pdf (16 pages, 238385 bytes). Transcript written on DESIGN.log. makeindex DESIGN.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file DESIGN.idx...done (0 entries accepted, 0 rejected). Nothing written in DESIGN.ind. Transcript written in DESIGN.ilg. pdflatex DESIGN.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./DESIGN.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) (./DESIGN.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./DESIGN.toc) [3] [4] Chapter 1. (./grid.tex [5] [6 <./adaptiveblock.pdf> <./adapted_grid.pdf>] [7 <./message_pa ss_equal.pdf> <./message_pass_res_change.pdf>]) (./temporal.tex LaTeX Warning: Reference `eq:continuity_conserve' on page 8 undefined on input line 16. LaTeX Warning: Reference `eq:energy_conserve' on page 8 undefined on input line 16. [8] [9]) (./spatial.tex [10 <./fivol.pdf>] [11] [12]) (./divb.tex LaTeX Warning: Reference `eq:momentum_conserve' on page 13 undefined on input l ine 34. LaTeX Warning: Reference `eq:energy_conserve' on page 13 undefined on input lin e 34. LaTeX Warning: Reference `eq:bfield_conserve' on page 13 undefined on input lin e 35. [13 <./slope.pdf>] [14] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [15]) [16] (./DESIGN.aux) LaTeX Warning: There were undefined references. ){/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on DESIGN.pdf (16 pages, 238807 bytes). Transcript written on DESIGN.log. makeindex DESIGN.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file DESIGN.idx...done (0 entries accepted, 0 rejected). Nothing written in DESIGN.ind. Transcript written in DESIGN.ilg. pdflatex DESIGN.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./DESIGN.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) (./DESIGN.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./DESIGN.toc) [3] [4] Chapter 1. (./grid.tex [5] [6 <./adaptiveblock.pdf> <./adapted_grid.pdf>] [7 <./message_pa ss_equal.pdf> <./message_pass_res_change.pdf>]) (./temporal.tex LaTeX Warning: Reference `eq:continuity_conserve' on page 8 undefined on input line 16. LaTeX Warning: Reference `eq:energy_conserve' on page 8 undefined on input line 16. [8] [9]) (./spatial.tex [10 <./fivol.pdf>] [11] [12]) (./divb.tex LaTeX Warning: Reference `eq:momentum_conserve' on page 13 undefined on input l ine 34. LaTeX Warning: Reference `eq:energy_conserve' on page 13 undefined on input lin e 34. LaTeX Warning: Reference `eq:bfield_conserve' on page 13 undefined on input lin e 35. [13 <./slope.pdf>] [14] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [15]) [16] (./DESIGN.aux) LaTeX Warning: There were undefined references. ){/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on DESIGN.pdf (16 pages, 238807 bytes). Transcript written on DESIGN.log. mv DESIGN.pdf ../ rm -f DESIGN.ind DESIGN.idx DESIGN.ilg touch STANDARDS.ind STANDARDS.idx pdflatex STANDARDS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./STANDARDS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) No file STANDARDS.aux. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] No file STANDARDS.toc. (./datanames.tex [3] [4] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [6] [7] [8] [9] [10] [11] [12] [13]) [14] (./STANDARDS.aux) ){/usr/share/texlive/texmf-dist/fon ts/enc/dvips/base/8r.enc} Output written on STANDARDS.pdf (14 pages, 96744 bytes). Transcript written on STANDARDS.log. makeindex STANDARDS.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file STANDARDS.idx...done (0 entries accepted, 0 rejected). Nothing written in STANDARDS.ind. Transcript written in STANDARDS.ilg. pdflatex STANDARDS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./STANDARDS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) (./STANDARDS.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./STANDARDS.toc) (./datanames.tex [3] [4] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [6] [7] [8] [9] [10] [11] [12] [13]) [14] (./STANDARDS.aux) ){/usr/share/texlive/texmf-dist/fon ts/enc/dvips/base/8r.enc} Output written on STANDARDS.pdf (14 pages, 97356 bytes). Transcript written on STANDARDS.log. makeindex STANDARDS.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file STANDARDS.idx...done (0 entries accepted, 0 rejected). Nothing written in STANDARDS.ind. Transcript written in STANDARDS.ilg. pdflatex STANDARDS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./STANDARDS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))))) (./STANDARDS.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./STANDARDS.toc) (./datanames.tex [3] [4] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [6] [7] [8] [9] [10] [11] [12] [13]) [14] (./STANDARDS.aux) ){/usr/share/texlive/texmf-dist/fon ts/enc/dvips/base/8r.enc} Output written on STANDARDS.pdf (14 pages, 97356 bytes). Transcript written on STANDARDS.log. mv STANDARDS.pdf ../ rm -f STANDARDS.ind STANDARDS.idx STANDARDS.ilg make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/Doc/Tex' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS' make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/doc/Tex' /homedata/gtoth/SWMFTEST/SWMF/share/Scripts/XmlToTex.pl */PARAM.XML > PWOMXML.tex touch PWOM.ind PWOM.idx pdflatex PWOM.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./PWOM.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) Writing index file PWOM.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (./html.sty) No file PWOM.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] No file PWOM.toc. [3]) (./PWOM_introduction.tex [4] Chapter 1. LaTeX Warning: Reference `SWMF' on page 5 undefined on input line 49. [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [6] Chapter 2. [7] [8] [9] LaTeX Warning: Reference `chapter:basics' on page 10 undefined on input line 31 7. LaTeX Warning: Reference `chapter:examples' on page 10 undefined on input line 320. ) [10] Chapter 3. (./PWOM_configuration.tex [11]) (./PWOM_param.tex [12]) [13] [14] Chapter 4. (./PWOM_SWMF.tex [15]) [16] Chapter 5. (./PWOM_example_runs.tex [17] [18]) [19] [20] Chapter 6. (./PWOMXML.tex [21] [22] [23] [24] [25] [26] [27]) (./PWOM.ind) (./PWOM.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) Output written on PWOM.pdf (27 pages, 166080 bytes). Transcript written on PWOM.log. makeindex PWOM.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file PWOM.idx....done (32 entries accepted, 0 rejected). Sorting entries....done (166 comparisons). Generating output file PWOM.ind....done (37 lines written, 0 warnings). Output written in PWOM.ind. Transcript written in PWOM.ilg. pdflatex PWOM.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./PWOM.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) Writing index file PWOM.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (./html.sty) (./PWOM.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./PWOM.toc) [3] [4]) (./PWOM_introduction.tex Chapter 1. [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [6] Chapter 2. [7] [8] [9]) [10] Chapter 3. (./PWOM_configuration.tex [11]) (./PWOM_param.tex [12]) [13] [14] Chapter 4. (./PWOM_SWMF.tex [15]) [16] Chapter 5. (./PWOM_example_runs.tex [17] [18]) [19] [20] Chapter 6. (./PWOMXML.tex [21] [22] [23] [24] [25] [26] [27]) (./PWOM.ind [28]) (./PWOM.aux) ) Output written on PWOM.pdf (28 pages, 167990 bytes). Transcript written on PWOM.log. makeindex PWOM.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file PWOM.idx....done (32 entries accepted, 0 rejected). Sorting entries....done (166 comparisons). Generating output file PWOM.ind....done (37 lines written, 0 warnings). Output written in PWOM.ind. Transcript written in PWOM.ilg. pdflatex PWOM.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./PWOM.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) Writing index file PWOM.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (./html.sty) (./PWOM.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (./PWOM.toc [3]) [4]) (./PWOM_introduction.tex Chapter 1. [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [6] Chapter 2. [7] [8] [9]) [10] Chapter 3. (./PWOM_configuration.tex [11]) (./PWOM_param.tex [12]) [13] [14] Chapter 4. (./PWOM_SWMF.tex [15]) [16] Chapter 5. (./PWOM_example_runs.tex [17] [18]) [19] [20] Chapter 6. (./PWOMXML.tex [21] [22] [23] [24] [25] [26] [27]) (./PWOM.ind [28]) (./PWOM.aux) ) Output written on PWOM.pdf (28 pages, 168036 bytes). Transcript written on PWOM.log. mv PWOM.pdf ../ rm -f PWOM.ind PWOM.idx PWOM.ilg make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/doc/Tex' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM' make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS' cd doc; make PDF make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS/doc' touch AMPS.ind AMPS.idx pdflatex AMPS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./AMPS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (./multirow.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Writing index file AMPS.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))) No file AMPS.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) [1 Non-PDF special ignored! papersize=8.5in,11in {/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}]pdfTeX warni ng (ext4): destination with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.26 \newpage [1] (./AMPS_introduction.tex Chapter 1. ) (./AMPS_Installation.tex [2] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 6--8 Underfull \hbox (badness 10000) in paragraph at lines 9--11 Underfull \hbox (badness 10000) in paragraph at lines 9--11 (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Underfull \hbox (badness 10000) in paragraph at lines 15--18 Underfull \hbox (badness 10000) in paragraph at lines 15--18 Overfull \hbox (8.60358pt too wide) in paragraph at lines 31--38 \OT1/cmtt/m/n/10.95 bullet\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 CG\OT1/cmr/m /n/10.95 , \OT1/cmtt/m/n/10.95 CouplerTest\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10 .95 Enceladus\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Europa\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Hartley2\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Hartley2 RotationBody\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Interface\OT1/cmr/m/n/10.9 5 , [3] Underfull \hbox (badness 10000) in paragraph at lines 38--43 Underfull \hbox (badness 10000) in paragraph at lines 38--43 Underfull \hbox (badness 10000) in paragraph at lines 52--53 Underfull \hbox (badness 10000) in paragraph at lines 53--54 Underfull \hbox (badness 10000) in paragraph at lines 54--55 Underfull \hbox (badness 10000) in paragraph at lines 55--56 Underfull \hbox (badness 10000) in paragraph at lines 56--57 Underfull \hbox (badness 10000) in paragraph at lines 57--58 [4] Underfull \hbox (badness 10000) in paragraph at lines 72--83 Underfull \hbox (badness 10000) in paragraph at lines 72--83 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 [5] Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 158--159 [6]) (./AMPS_InputCommands.tex [7] Chapter 3. [8] [9] Overfull \hbox (143.6891pt too wide) in paragraph at lines 138--139 \OT1/cmr/m/n/10.95 tion.Exosphere.h", "UserDef-i-ni-tion.meshAMR.h", "UserDef-i -ni-tion.PIC.h", and "UserDef-i-ni-tion.PIC.PhysicalModelHeaderList.h" [10] [11] [12] Overfull \hbox (0.17108pt too wide) in paragraph at lines 262--263 \OT1/cmr/m/n/10.95 The sec-tion con-trols the non-standard AMPS sam-pling rou-t ines. The sec-tion be-gins with \OT1/cmtt/m/n/10.95 #Sampling [13] [14] Overfull \hbox (3.80275pt too wide) in paragraph at lines 354--355 \OT1/cmr/m/n/10.95 Describes the func-tions that are used for mod-el-ing of the pho-tolytic re-ac-tions (photo-ionization, [15] Overfull \hbox (75.60896pt too wide) in paragraph at lines 383--384 []\OT1/cmr/bx/n/10.95 Source:PhotonStimulatedDesorption\OT1/cmr/m/n/10.95 = [on ,off],PhotonFlux=[],CrossSection[],InjectionVelocityRange=[] [16] Overfull \hbox (23.26375pt too wide) in paragraph at lines 402--403 \OT1/cmtt/m/n/10.95 InitSurfaceSourceDistribution=HeliumDesorption::SurfaceInje ctionDistribution.Init ) (./AMPS_Examples.tex [17] Chapter 4. Package natbib Warning: Citation `Lamy-2006-AA' on page 18 undefined on input l ine 7. Package natbib Warning: Citation `Davidsson-2004-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Tenishev-2008-AJ' on page 18 undefined on inp ut line 7. Package natbib Warning: Citation `Tenishev-2011-AJ' on page 18 undefined on inp ut line 7. Package natbib Warning: Citation `Lamy-2006-AA' on page 18 undefined on input l ine 18. Package natbib Warning: Citation `Crovisier-1984-AA' on page 18 undefined on in put line 34. [18] Package natbib Warning: Citation `Davidsson-2004-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2004-icarus' on page 19 undefined o n input line 47. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 19 undefined o n input line 47. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 19 undefined o n input line 47. [19]) No file AMPS.bbl. Package natbib Warning: There were undefined citations. [20] (./AMPS.aux) Package rerunfilecheck Warning: File `AMPS.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on AMPS.pdf (21 pages, 216916 bytes). Transcript written on AMPS.log. makeindex AMPS.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file AMPS.idx...done (0 entries accepted, 0 rejected). Nothing written in AMPS.ind. Transcript written in AMPS.ilg. pdflatex AMPS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./AMPS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (./multirow.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Writing index file AMPS.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))) (./AMPS.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./AMPS.out) (./AMPS.out) [1 Non-PDF special ignored! papersize=8.5in,11in {/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] (./AMPS.toc )pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.26 \newpage [1] (./AMPS_introduction.tex Chapter 1. ) (./AMPS_Installation.tex [2] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 6--8 Underfull \hbox (badness 10000) in paragraph at lines 9--11 Underfull \hbox (badness 10000) in paragraph at lines 9--11 (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Underfull \hbox (badness 10000) in paragraph at lines 15--18 Underfull \hbox (badness 10000) in paragraph at lines 15--18 Overfull \hbox (8.60358pt too wide) in paragraph at lines 31--38 \OT1/cmtt/m/n/10.95 bullet\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 CG\OT1/cmr/m /n/10.95 , \OT1/cmtt/m/n/10.95 CouplerTest\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10 .95 Enceladus\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Europa\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Hartley2\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Hartley2 RotationBody\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Interface\OT1/cmr/m/n/10.9 5 , [3] Underfull \hbox (badness 10000) in paragraph at lines 38--43 Underfull \hbox (badness 10000) in paragraph at lines 38--43 Underfull \hbox (badness 10000) in paragraph at lines 52--53 Underfull \hbox (badness 10000) in paragraph at lines 53--54 Underfull \hbox (badness 10000) in paragraph at lines 54--55 Underfull \hbox (badness 10000) in paragraph at lines 55--56 Underfull \hbox (badness 10000) in paragraph at lines 56--57 Underfull \hbox (badness 10000) in paragraph at lines 57--58 [4] Underfull \hbox (badness 10000) in paragraph at lines 72--83 Underfull \hbox (badness 10000) in paragraph at lines 72--83 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 [5] Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 158--159 [6]) (./AMPS_InputCommands.tex [7] Chapter 3. [8] [9] Overfull \hbox (143.6891pt too wide) in paragraph at lines 138--139 \OT1/cmr/m/n/10.95 tion.Exosphere.h", "UserDef-i-ni-tion.meshAMR.h", "UserDef-i -ni-tion.PIC.h", and "UserDef-i-ni-tion.PIC.PhysicalModelHeaderList.h" [10] [11] [12] Overfull \hbox (0.17108pt too wide) in paragraph at lines 262--263 \OT1/cmr/m/n/10.95 The sec-tion con-trols the non-standard AMPS sam-pling rou-t ines. The sec-tion be-gins with \OT1/cmtt/m/n/10.95 #Sampling [13] [14] Overfull \hbox (3.80275pt too wide) in paragraph at lines 354--355 \OT1/cmr/m/n/10.95 Describes the func-tions that are used for mod-el-ing of the pho-tolytic re-ac-tions (photo-ionization, [15] Overfull \hbox (75.60896pt too wide) in paragraph at lines 383--384 []\OT1/cmr/bx/n/10.95 Source:PhotonStimulatedDesorption\OT1/cmr/m/n/10.95 = [on ,off],PhotonFlux=[],CrossSection[],InjectionVelocityRange=[] [16] Overfull \hbox (23.26375pt too wide) in paragraph at lines 402--403 \OT1/cmtt/m/n/10.95 InitSurfaceSourceDistribution=HeliumDesorption::SurfaceInje ctionDistribution.Init ) (./AMPS_Examples.tex [17] Chapter 4. Package natbib Warning: Citation `Lamy-2006-AA' on page 18 undefined on input l ine 7. Package natbib Warning: Citation `Davidsson-2004-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Tenishev-2008-AJ' on page 18 undefined on inp ut line 7. Package natbib Warning: Citation `Tenishev-2011-AJ' on page 18 undefined on inp ut line 7. Package natbib Warning: Citation `Lamy-2006-AA' on page 18 undefined on input l ine 18. Package natbib Warning: Citation `Crovisier-1984-AA' on page 18 undefined on in put line 34. [18] Package natbib Warning: Citation `Davidsson-2004-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2004-icarus' on page 19 undefined o n input line 47. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 19 undefined o n input line 47. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 19 undefined o n input line 47. [19]) No file AMPS.bbl. Package natbib Warning: There were undefined citations. [20] (./AMPS.aux) ) (see the transcript file for additional information) Output written on AMPS.pdf (21 pages, 221419 bytes). Transcript written on AMPS.log. makeindex AMPS.idx This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). Scanning input file AMPS.idx...done (0 entries accepted, 0 rejected). Nothing written in AMPS.ind. Transcript written in AMPS.ilg. pdflatex AMPS.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./AMPS.tex LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (./multirow.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Writing index file AMPS.idx (./HEADER.tex (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))) (./AMPS.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./AMPS.out) (./AMPS.out) [1 Non-PDF special ignored! papersize=8.5in,11in {/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] (./AMPS.toc )pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.26 \newpage [1] (./AMPS_introduction.tex Chapter 1. ) (./AMPS_Installation.tex [2] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 6--8 Underfull \hbox (badness 10000) in paragraph at lines 9--11 Underfull \hbox (badness 10000) in paragraph at lines 9--11 (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Underfull \hbox (badness 10000) in paragraph at lines 15--18 Underfull \hbox (badness 10000) in paragraph at lines 15--18 Overfull \hbox (8.60358pt too wide) in paragraph at lines 31--38 \OT1/cmtt/m/n/10.95 bullet\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 CG\OT1/cmr/m /n/10.95 , \OT1/cmtt/m/n/10.95 CouplerTest\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10 .95 Enceladus\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Europa\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Hartley2\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Hartley2 RotationBody\OT1/cmr/m/n/10.95 , \OT1/cmtt/m/n/10.95 Interface\OT1/cmr/m/n/10.9 5 , [3] Underfull \hbox (badness 10000) in paragraph at lines 38--43 Underfull \hbox (badness 10000) in paragraph at lines 38--43 Underfull \hbox (badness 10000) in paragraph at lines 52--53 Underfull \hbox (badness 10000) in paragraph at lines 53--54 Underfull \hbox (badness 10000) in paragraph at lines 54--55 Underfull \hbox (badness 10000) in paragraph at lines 55--56 Underfull \hbox (badness 10000) in paragraph at lines 56--57 Underfull \hbox (badness 10000) in paragraph at lines 57--58 [4] Underfull \hbox (badness 10000) in paragraph at lines 72--83 Underfull \hbox (badness 10000) in paragraph at lines 72--83 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 Underfull \hbox (badness 10000) in paragraph at lines 86--111 [5] Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 130--156 Underfull \hbox (badness 10000) in paragraph at lines 158--159 [6]) (./AMPS_InputCommands.tex [7] Chapter 3. [8] [9] Overfull \hbox (143.6891pt too wide) in paragraph at lines 138--139 \OT1/cmr/m/n/10.95 tion.Exosphere.h", "UserDef-i-ni-tion.meshAMR.h", "UserDef-i -ni-tion.PIC.h", and "UserDef-i-ni-tion.PIC.PhysicalModelHeaderList.h" [10] [11] [12] Overfull \hbox (0.17108pt too wide) in paragraph at lines 262--263 \OT1/cmr/m/n/10.95 The sec-tion con-trols the non-standard AMPS sam-pling rou-t ines. The sec-tion be-gins with \OT1/cmtt/m/n/10.95 #Sampling [13] [14] Overfull \hbox (3.80275pt too wide) in paragraph at lines 354--355 \OT1/cmr/m/n/10.95 Describes the func-tions that are used for mod-el-ing of the pho-tolytic re-ac-tions (photo-ionization, [15] Overfull \hbox (75.60896pt too wide) in paragraph at lines 383--384 []\OT1/cmr/bx/n/10.95 Source:PhotonStimulatedDesorption\OT1/cmr/m/n/10.95 = [on ,off],PhotonFlux=[],CrossSection[],InjectionVelocityRange=[] [16] Overfull \hbox (23.26375pt too wide) in paragraph at lines 402--403 \OT1/cmtt/m/n/10.95 InitSurfaceSourceDistribution=HeliumDesorption::SurfaceInje ctionDistribution.Init ) (./AMPS_Examples.tex [17] Chapter 4. Package natbib Warning: Citation `Lamy-2006-AA' on page 18 undefined on input l ine 7. Package natbib Warning: Citation `Davidsson-2004-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 18 undefined o n input line 7. Package natbib Warning: Citation `Tenishev-2008-AJ' on page 18 undefined on inp ut line 7. Package natbib Warning: Citation `Tenishev-2011-AJ' on page 18 undefined on inp ut line 7. Package natbib Warning: Citation `Lamy-2006-AA' on page 18 undefined on input l ine 18. Package natbib Warning: Citation `Crovisier-1984-AA' on page 18 undefined on in put line 34. [18] Package natbib Warning: Citation `Davidsson-2004-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 19 undefined o n input line 38. Package natbib Warning: Citation `Davidsson-2004-icarus' on page 19 undefined o n input line 47. Package natbib Warning: Citation `Davidsson-2005-icarus' on page 19 undefined o n input line 47. Package natbib Warning: Citation `Davidsson-2006-icarus' on page 19 undefined o n input line 47. [19]) No file AMPS.bbl. Package natbib Warning: There were undefined citations. [20] (./AMPS.aux) ) (see the transcript file for additional information) Output written on AMPS.pdf (21 pages, 221419 bytes). Transcript written on AMPS.log. mv AMPS.pdf ../ rm -f AMPS.ind AMPS.idx AMPS.ilg make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS/doc' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS' rm -rf *~ doc/*~ Param/*~ TAGS for i in `ls -d [A-Z][A-Z]/*/`; \ do (echo Cleaning $i; cd $i; make clean); done Cleaning CZ/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CZ/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CZ/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CZ/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CZ/Empty' Cleaning EE/BATSRUS/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/EE/BATSRUS' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/EE/BATSRUS' Cleaning EE/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/EE/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/EE/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/EE/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/EE/Empty' Cleaning GM/BATSRUS/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex rm -rf Tmp_ make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/src' cd srcBATL; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/srcBATL' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/srcBATL' cd srcInterface; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/srcInterface' cd srcPostProc; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/srcPostProc' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS/srcPostProc' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/BATSRUS' Cleaning GM/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/GM/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/GM/Empty' Cleaning IE/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Empty' Cleaning IE/Ridley_serial/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Ridley_serial' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Ridley_serial/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Ridley_serial/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IE/Ridley_serial' Cleaning IH/BATSRUS/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IH/BATSRUS' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IH/BATSRUS' Cleaning IH/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IH/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IH/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IH/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IH/Empty' Cleaning IM/CIMI/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI/src' cd srcGIMME; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI/srcGIMME' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI/srcGIMME' cd srcInterface; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI/srcInterface' cd doc/Tex; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI/doc/Tex' rm -f *.out *.aux *.log *.toc *.ind *.idx *.ilg *.dvi *.ps *~ *.protex rm -f CIMIXML.tex rm -f CIMIREF CIMIXML make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI/doc/Tex' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/CIMI' Cleaning IM/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/Empty' Cleaning IM/HEIDI/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/HEIDI' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/HEIDI/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/HEIDI/src' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/HEIDI/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/HEIDI/srcInterface' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/HEIDI' Cleaning IM/RCM2/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/RCM2' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/RCM2/src' Makefile:75: warning: overriding recipe for target '.f90.o' /homedata/gtoth/SWMFTEST/SWMF/Makefile.conf:73: warning: ignoring old recipe for target '.f90.o' Makefile:79: warning: overriding recipe for target '.f.o' /homedata/gtoth/SWMFTEST/SWMF/Makefile.conf:79: warning: ignoring old recipe for target '.f.o' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/RCM2/src' cd src/claw; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/IM/RCM2/src/claw' Makefile:36: warning: overriding recipe for target '.f.o' /homedata/gtoth/SWMFTEST/SWMF/Makefile.conf:79: warning: ignoring old recipe for target '.f.o' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/RCM2/src/claw' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/IM/RCM2' Cleaning OH/BATSRUS/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/OH/BATSRUS' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/OH/BATSRUS' Cleaning OH/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/OH/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/OH/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/OH/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/OH/Empty' Cleaning PC/ALTOR/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR/src' cd srcInterface; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR/srcInterface' cd srcBATL_orig; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR/srcBATL_orig' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR/srcBATL_orig' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR/srcBATL' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR/srcBATL' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/ALTOR' Cleaning PC/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/Empty' Cleaning PC/FLEKS/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/FLEKS' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/FLEKS/src' make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/FLEKS/src' cd srcInterface; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PC/FLEKS/srcInterface' make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/FLEKS/srcInterface' rm -rf bin/* make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PC/FLEKS' Cleaning PS/DGCPM/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PS/DGCPM' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PS/DGCPM/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PS/DGCPM/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PS/DGCPM' Cleaning PS/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PS/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PS/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PS/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PS/Empty' Cleaning PT/AMPS/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS' rm -rf build/libAMPS.a build make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS/srcInterface' cd doc; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS/doc' rm -f AMPS.aux AMPS.log AMPS.out AMPS.toc make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS/doc' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/AMPS' Cleaning PT/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/Empty' Cleaning PT/FLEKS/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/FLEKS' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/FLEKS/src' make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/FLEKS/src' cd srcInterface; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/FLEKS/srcInterface' make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/FLEKS/srcInterface' rm -rf bin/* make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/FLEKS' Cleaning PT/PARMISAN/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/PARMISAN' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/PARMISAN/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/PARMISAN/src' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PT/PARMISAN/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/PARMISAN/srcInterface' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PT/PARMISAN' Cleaning PW/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/Empty' Cleaning PW/PWOM/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex rm -rf Tmp_ make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/src' cd srcSTET; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcSTET' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcSTET' cd srcTWOSTREAM; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcTWOSTREAM' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcTWOSTREAM' cd srcGITMREADER; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcGITMREADER' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcGITMREADER' cd srcInterface; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcInterface' cd doc/Tex; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/doc/Tex' rm -f *.out *.aux *.log *.toc *.ind *.idx *.ilg *.dvi *.ps *~ *.protex rm -f PWOMXML.tex rm -f PWOMREF PWOMXML make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/doc/Tex' cd srcPostProc; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcPostProc' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM/srcPostProc' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/PW/PWOM' Cleaning RB/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/RB/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/RB/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/RB/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/RB/Empty' Cleaning RB/RBE/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/RB/RBE' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/RB/RBE/src' Makefile:31: warning: overriding recipe for target '.f.o' /homedata/gtoth/SWMFTEST/SWMF/Makefile.conf:79: warning: ignoring old recipe for target '.f.o' Makefile:34: warning: overriding recipe for target '.f90.o' /homedata/gtoth/SWMFTEST/SWMF/Makefile.conf:73: warning: ignoring old recipe for target '.f90.o' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/RB/RBE/src' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/RB/RBE/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/RB/RBE/srcInterface' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/RB/RBE' Cleaning SC/BATSRUS/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SC/BATSRUS' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SC/BATSRUS' Cleaning SC/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SC/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SC/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SC/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SC/Empty' Cleaning SP/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SP/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SP/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SP/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SP/Empty' Cleaning SP/MFLAMPA/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SP/MFLAMPA' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SP/MFLAMPA/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SP/MFLAMPA/src' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/SP/MFLAMPA/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SP/MFLAMPA/srcInterface' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/SP/MFLAMPA' Cleaning UA/Empty/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/Empty' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/Empty/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/Empty/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/Empty' Cleaning UA/GITM/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM' cd srcSphereAB; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM/srcSphereAB' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM/srcSphereAB' cd src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM/src' cd srcGlow; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM/srcGlow' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM/srcGlow' cd srcInterface; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM/srcInterface' if [ -d share ]; then cd share; make cleanall; fi; if [ -d util ]; then cd util; make cleanall; fi; if [ -d srcSAMI ]; then cd srcSAMI; make clean; fi; make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM' Cleaning UA/GITM2/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2/srcSphereAB' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2/srcSphereAB' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2/src' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2/srcGlow' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2/srcGlow' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2/srcInterface' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/GITM2' Cleaning UA/MGITM/ make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM/srcSphereAB' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM/srcSphereAB' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM/src' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM/srcGlow' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM/srcGlow' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM/srcInterface' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM/srcInterface' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/UA/MGITM' cd CON; make clean make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CON' cd Control/src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Control/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex rm -rf Tmp_* make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Control/src' cd Library/src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Library/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Library/src' cd Coupler/src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Coupler/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Coupler/src' cd Interface/src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Interface/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Interface/src' cd Stubs/src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Stubs/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CON/Stubs/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/CON' cd share; make clean make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/share' cd Library/src; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/share/Library/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/share/Library/src' cd Library/test;make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/share/Library/test' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/share/Library/test' cd Prologs; make clean make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/share/Prologs' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/share/Prologs' rm -f include/*.mod make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/share' cd util; make clean make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/NOMPI/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/NOMPI/src' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/TIMING' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/TIMING/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/TIMING/src' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/TIMING/srcEmpty' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/TIMING/srcEmpty' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/TIMING/doc' /bin/rm -f *.log *.aux *.dvi *~ make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/TIMING/doc' make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/TIMING' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/DATAREAD' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/DATAREAD/srcIndices' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/DATAREAD/srcIndices' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/DATAREAD/srcMagnetogram' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/DATAREAD/srcMagnetogram' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/DATAREAD/srcDemt' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/DATAREAD/srcDemt' make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/DATAREAD' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcCosmicRay' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcCosmicRay' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcEE' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcEE' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcIE' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcIE' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcGM' Makefile:16: warning: overriding recipe for target '.f.o' ../../../Makefile.conf:79: warning: ignoring old recipe for target '.f.o' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcGM' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcSC' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcSC' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcUA' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL/srcUA' make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/EMPIRICAL' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/CRASH' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/CRASH/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/CRASH/src' make[3]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/CRASH/doc/Tex' rm -f *.log *.aux *~ make[3]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/CRASH/doc/Tex' make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/CRASH' make[2]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/util/FISHPAK/src' rm -f *~ core *.o *.mod fort.* a.out *.exe *.a *.so *.protex make[2]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util/FISHPAK/src' make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/util' cd doc/Tex; make clean make[1]: Entering directory '/homedata/gtoth/SWMFTEST/SWMF/doc/Tex' rm -f *.out *.aux *.log *.toc *.ind *.idx *.ilg *.dvi *.ps *~ *.protex rm -f SWMFREF.tex SWMFXML.tex SWPC.XML SWPCXML.tex BATSRUS_SCRIPTS.tex rm -f SWMFREF SWMFXML SWPCXML BATSRUS_SCRIPTS make[1]: Leaving directory '/homedata/gtoth/SWMFTEST/SWMF/doc/Tex' cd bin; rm -f *.exe cd lib; rm -f *.a *.so Clean succeeded