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User's Manual - Carl von Ossietzky Universität Oldenburg

1. Phosphate Nip Box 1 mmol m3 Nitrate N3n Box 1 mmol m3 0 87 11 30 o GR y A Lob de ry 0 72 NN Eince15 9 42 aa Once15 0 58 7 53 l5 _ 4 D in a a 0 43 H 5 65 il a n E 0 29 m e 3 77 RO B Se D amp B ft JU EE m 0 14 1 88 i DUM KAL m i 0 00 RE YY fi 0 00 j om 1 60 12 180 240 360 0 60 12 180 240 300 360 Ammonium N4n Box 1 mmol m3 Silicate Nbs Box 1 mmol m3 2 33 6 41 b result E L bil result emiri ia ni89 EE sedisse nlBg 1 94 ince15 i N 5 34 Cincet5 155 oy 427 NN EI Ber er 146 N T RH 3 20 m E F 5 Kal F Ses ie s JEN 4E 0 78 i fi N 244 I i li E L i j L i pe Y A SN Te rm 07 k a NE 0 39 ch m P ei Bomam m aiv F F NES ERO 0 00 Ne AS Me s drug 0 00 E 60 120 180 240 300 360 0 60 120 180 240 300 360 XVGRIMoViE TK Graphic Figure 6 1 A plot from the compare tool A comparison of model results and field measurements is shown This tool allows a comparison of different result files and the comparison of model results and field measurements For the format of these data sets see appendix 17 The compare tool allows also the comparison of different periods of f e the same result file to investigate the temporal cha
2. The Film Tool Record to PostScript starts the animation and writes the whole animation into a PostScript file The output files are named mov_x ps and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased Snapshot to PostScript prints the actual picture into a PostScript file The output files are named mov_x ps and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased Remark The PostSript options must be handled with care considering the available space on the hard disk Due to the automatic naming of the files existing files may be overwritten 7 1 The control panel MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 8 The Text Tool 8 The Text Tool This tool provides a view on the numerical values of all results in up to three result files It is built for mass conservation checks and program checking It allows adding of variables multiplying variables by a scalar and a brief statistical analysis Text Area The text area is a scrollable window where the numerical output is printed column by column It is possible to mark text in it and copy it to other applications etc Text control panel 1 fix variable _ fix boxes J act on all columns EE Format oo vsva fve Set time window 380 2358 Select starttime 0 Decimal Places
3. data to fourier Transforms a whole symb file into spectral values and stores them in a _pk outc file The transformation method is described in 1991 The pk files are read by every tool and will be synthesized automatically With this transformation results and field data become mathematically comparerable This is the base for using the functionality of the L2 Distance functions on results and data The compare tool and the text tool provide the functionality of showing the spectral values themselves After selection of the symb file MoViE asks for some basic data for transformation These values has to be adapted to the future use of the created _pk outc file cycle This value defines the fundamental wavelength which will be used for the synthesis of the analyzed data sets outdelt This value defines the resolution of the synthesis The default is 0 1 epsi This value controls the smoothness of the analysis of non equidistant data sets The default value 1 gives control to the transformation rou tine to evaluate this value from the statistical variance of the data This is a good choice in most cases For manual adjustments of this parameter number of harmonics This parameter determines how many harmonics shall be stored in the _pk outc file The default value 1 gives control to the transformation routine to evaluate this value from the number of samples according to the sampling theorem This is a good choice in most
4. Figure 8 1 Control panel of the text tool The control panel contains all buttons and sliders for modifying the numerical output Select starttime and Set time window The starting time of the plot and the period which shall be plotted can be selected If the time window exceeds the endtime for a starttime the time window will be reduced accordingly Chapter 8 The Text Tool MoViE User s Manual August 26 2012 new column The next selected variable will be printed in an additional column Here a column must be understood as a block of x columns where x denotes the number of loaded files The same action can be activated by a right mouse click on the variable box Remark The blocks of columns are structural identical to the graphs in the compare tool In the following a column means a block of columns if not specified differently All modifications as f e changing the variable will be done in this column block until new column is pressed again There is an internal limitation of 9 columns blocks erase column Only active if two or more columns are printed Deletes successively the last column The next operations will affect the new last column erase all Only active if two or more columns are printed All displayed columns will be deleted fix variables The variable selector will become inactive and the present selection of variables will be fixed for the next actions After selectin
5. These buttons activate apply show borderlines If activated border lines are displayed during animation show boxnumbers If activated box numbers are displayed after animation mark zero values If activated zeros are displayed in grey and not in a color of the color table Color table tracer opens a menu with different color tables which can be selected This must be confirmed by apply Remark Only valid for ECOTIM If an EulerBox variable is selected and the corresponding values for all voxels are stored including the xcoor and ycoor variables the tracers are animated Choose map Normally MoViE loads the correct setup automatically Here it can be set by hand This must be confirmed by apply Color table apply opens a menu with different color tables which can be selected This must be confirmed by apply The map the boxes and the selected variable at the selected starttime will be drawn The color bar shows the range of values and the corresponding color After every modification which affects the actual selection such as changes in the selected variable starting time lower or upper boxes and re scalings this 7 1 The control panel MoViE User s Manual August 26 2012 button becomes active and must be pressed before the next animation It takes care that the given colors and color ranges names and units correspond to the actual choice This avoid unnecessary dat
6. 7 are stored as floats in binary format 8 the word fourier as a string of 80 twelve in xxx outb characters to identify that this file contains spectrum data the word fourier is filled with spaces to make up a string of 80 resp twelve characters This header is followed by a set of nvars strings of each 80 twelve in xxx outb ASCII characters These strings are containing the name of a variable and the box number for which it is stored e p1ic 137 indicates plc of box 137 being stored After this block of strings which may be some ten kilobytes long the spectrum data are stored as follows One float is stored in binary format for each variable box combination appearing in the string block 9 One block is stored for each base vector from O to number of base vectors 4 This block may have a length of several megabytes 17 3 xxx nc MoViE User s Manual August 26 2012 17 3 xxx nc MoViE also reads NetCDF files of the format described in the following A complete specification of the NetCDF interface in the used version 3 5 1 is given in x Here the variables and their types as used by CEMoS and read by MoViE are For the data formats of NC_CHAR 1997 NC INT and NC FLOAT see NetCDF global attributes One global attribute is set by CEMOS NC_CHAR originator created by TIGERGRAPHICS CEMoS dimensions The dimension of time information appears as follows time_dim UNLIMITED thi
7. are replaced by the next selected one act on all graphs This button becomes active if fix boxes or fix variables is selected If act on all graphs is pressed the fixes in variables or boxes will act on all displayed graphs Pressing act on all graphs again deactivates this option The fixes will work on the last the actual graph only again smooth If smooth is active the data points will be spline interpolated otherwise they will be displayed as a polygon direct apply If direct apply is active all clicks in the box selector or the variable selector as well as all actions on the different sliders will be immediately evaluated If direct apply is not active the actual settings also creation of new sets or graphs will be evaluated when the button Apply is pressed Such it is possible to prepare more complex displays in a kind of offline mode and get the results displayed in one evaluation Analysis See chapter 15 command See chapter MoViE User s Manual August 26 2012 Chapter 11 The Phase Tool PS print A PostScript output to an external file will be produced The output files are named mov_x ps and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased Grace print This button acts similar to PS print but instead of sending the screens contents to the printer or storing it as PostScript code into a file
8. Grace print This button acts similar to PS print but instead of sending the screens contents to the printer or storing it as PostScript code into a file it produces an xmGrace rp output with all relevant information for legends and labels and stores it into an external file Ihttp plasma ate weizmann ac il Grace xmGrace is not available for Windows sys 8 tems Chapter 5 The Overview Tool MoViE User s Manual August 26 2012 The output files are named mov_x agr and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased xmGrace allows the free arrangement of graphs the modification of colours and linestyles tick marks and tick labels titles and legends Additionally it has several features for further statistical analysis and output formats Set Label Additional text can be added to the plot in different fontsizes The text must be given in the text field After confirming this by ENTER the text appears in the drawing area It can be moved by pressing the left mouse button on it and moving the mouse holding the button pressed After releasing the mouse button the title jumps to that position The label can be removed by a right mouse click while holding the shift button pressed The label will appear in the PostScript outputs but not in the xmGrace files MoViE User s Manual August 26 2012 Chapter 6 The Compare Tool 6 The Compare Tool
9. MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 16 command 16 command This button opens a window that enables the user to produce outputs with a maximum of nine predefined commands see Figure 16 Command Control i nb x _ Load Save Close Selected Mode Recall An 1 ie nasty 2 mpQ n3 namQ nssQ ED Do E Or Ec Bloc Figure 16 1 Command control panel Command sequences for up to nine graphs with each up to twenty variables to be displayed can be stored in files and read from files such the user is able to setup often used sequences for different purposes without starting from scratch with every MoViE session In addition to the very simple formulas which can be produced with the Anal ysis tool see section 15 the command tool offers the possibility of editing formulas in the command text fields Those formulas are then interpreted by MoViE such the complete range of mathematical expressions including brackets is allowed Note These formulas must not contain any white space since this is the set separator within one graph Note The user has to take care for the correctness and the syntax of those formulas In case of errors MoViE will not crash but will display an error message in the Info Window which might not be very helpful Chapter 16 command MoViE User s Manual August 26 2012 load commands
10. and save commands A file selector box is opened from where the command lines can be read or stored from into an external file Files holding those commands have the extension mcf MoViE Command File By default mcf files are either stored in the actual working direc tory from where the MoViE session was started or if existing in a directory mcf in the actual working directory The structure of the mcf is given in 17 5 Close Closes the command tool window The actual commands will be held in the text lines until the MoViE session is finished Recall Store This button changes the mode of work of the command tool If the button shows Recall the numbered buttons below and the All button right of this are recalling the command sequence s shown in the text lines of the command window If the button shows Store the command sequence of the actual graph can be stored into a text line by selecting one of the numbered buttons 1 9 If All is pressed command lines corresponding to all visible graphs are stored into the adequate number of text lines starting with 1 This may overwrite existing commands Command lines can be saved into a file by save commands and read from files by load commands Store does not stay active after one storing action but returns automatically into Recall model Commands for up to 20 sets per graph can be recalled stored One text line resp one sin
11. erase all graphs or if only one active graph remains in the drawing area erase all graphs This button erases all graphs with all their sets This is useful to clear up the drawing area if you are loosing the overview eval layer If eval layer is selected and if the result file contains information on the layer thickness stored in the variable layer the information on time changing layer thicknesses are evaluated to compose the plot of the profile If the variable Chapter 10 The ProfCom Tool MoViE User s Manual August 26 2012 layer is not stored or if eval layer is not activated all layer thicknesses are assumed to be equal and constant show layer value If show layer value is selected and if the result file contains information on the layer thickness stored in the variable layer the information on time changing layer thicknesses are evaluated and the depth starting from top is displayed on the layer axis instead of the layer number flip x y Change to a plot with exchanged concentration and layer axes same x axis If this option is active all graphs in the drawing area get the same scaling on the x axis This is useful if the same variable is drawn for different boxes scale to time maximum If this option is active the x axis maximum is set to the maximum over the whole time interval Barchart The data will be displayed as barcharts instead of lines smooth If smooth is acti
12. 0 60 120 180 240 300 360 0 120 180 240 300 360 2543 78 Flagellates P2c Box 8 mgC m3 109 73 Kemik Flagellates Pac Box5 mgCim3 2119 82 i i FiagellatesP2c Box15 mgC m3 87 78 1695 85 E 65 84 n 1271 89 43 89 847 93 F Infaunal Predators Y5 Box 8 mgC m2 21 95 423 96 lt lt Infaunal Predators Y5c Box 15 mgC m2 ga EZ L 0 00 Loau I SEY 0 00 0 60 120 180 240 300 360 0 60 120 180 240 300 360 XVGRIMoViE TK Graphic Figure 5 1 A multi graph plot from the overview tool This tool allows a close look to the change in time of every stored variable in each box It is possible to have a look on several variables in one graph These variables might be of one box or of different boxes After selecting a set of variables boxes these can be fixed and can be shown for different boxes variables Starttime and a time window can be selected to show only temporal parts of the simulation results Time plots are displayed for the selected variables in the selected boxes The axis labels of the time axis are set automatically in respect to the information within the result file and the stored time interval By means of the file name info see 17 6 variable names from simulations may be translated to extended names with units MoViE will read this file and the full name and the unit of the variable will be displayed if available and reasonable If no informa
13. 3 n3n 3 pic 1 100 0 empty empty empty empty empty 17 6 name info MoViE User s Manual August 26 2012 17 6 name info In this file the information is stored about the variables that may occur in the user s model output The file contains pure ASCII data Those data shall be organized as follows 1st column Short name of the variable appearing in the model s output 2nd column Description of the variable s meaning 3rd column Unit of the variable 4th column Identifier for type e g benthic or pelagic or none 5th column Identifier for the index box number e g p1c 134 to identify whether this number should be understood as a box number EulerBox as a voxel number Voxel or as a layer number Layer The columns must be separated by a colon such the colon is not allowed in a name of a variable a description or a unit For example Nip Phosphate Nip mmol m3 pelagic Voxel results in the following head line for e g N1p 13 in MoViE canvases Phosphate Nip Vozel 13 mmol m3 and A2c Benthic Non Diatoms A2c mgC m2 benthic EulerBox results in the following head line for e g A2c 25 in MoViE canvases Benthic Non Diatoms A2c EulerBox 25 mgC m2 The normal head line in absence of name info will simply be N1p 13 and A2c 25 One default name info comes with the MoViE package It is located in TKMOVIEHOME info If a name info is present in a model directory this local on
14. MoViE User s Manual August 26 2012 eval layer If eval layer is selected and if the result file contains information on the layer thickness stored in the variable layer the information on time changing layer thicknesses are evaluated to compose the plot of the profile If the variable layer is not stored or if eval layer is not activated all layer thicknesses are assumed to be equal and constant show layer value If show layer value is selected and if the result file contains information on the layer thickness stored in the variable layer the information on time changing layer thicknesses are evaluated and the depth starting from top is displayed on the layer axis instead of the layer number Hip x y Change to a plot with exchanged concentration and layer axes same x axis If this option is active all graphs in the drawing area get the same scaling on the x axis This is useful if the same variable is drawn for different boxes scale to time maximum If this option is active the x axis maximum is set to the maximum over the whole time interval Barchart The data will be displayed as barcharts instead of lines smooth If smooth is active the data points will be spline interpolated otherwise they will be displayed as a polygon MoViE User s Manual August 26 2012 Chapter 9 The Profile Tool direct apply If direct apply is active all clicks in the box selector or the variabl
15. Tool control Cancel Clicking Cancel leave this tool without applying any changes to the tkmoviedefaults Apply amp Exit Clicking Apply amp Exit immediately applies the settings tkmoviedefaults and leaves this tool MoViE User s Manual August 26 2012 Chapter 14 The Prepare Tool 14 The Prepare Tool The prepare tool provides auxiliary tools for transforming result and data files Tiger Graphics Prepare Tool Figure 14 1 Prepare tool info window All program output is shown here if the program is not started in background start in background If activated all programs are started in background result to fourier Transforms a whole outc file into spectral values and stores them in a _pk outc file The transformation method is described in 1991 The pk files are read by every tool and will be synthesized automatically They built the base for the functionality of the L2 Distance functions The compare Chapter 14 The Prepare Tool MoViE User s Manual August 26 2012 tool and the text tool provide the functionality of showing the spectral values themselves The program doing the transformation calculates a transformation matrix that is only dependent on the number of data samples Since the calculation of this matrix may take a quite long time up to some hours it is stored in a directory MOVIE matrices to be re used for transforming result files with the same number of samples
16. cases All values can be put into the according text fields and must be confirmed by ENTER MoViE User s Manual August 26 2012 Chapter 14 The Prepare Tool Cancel Cancel stops the selection and the process OK OK sends the a m values to the transformation routine and starts the transformation result to csv and data to csv Converts outc outb resp symb files into csv files comma separated values This format can be read by most of all spreadsheet programs The files are named similar to the source files but with the extension csv Remark If you are using the German version of a spread sheet program you must take care that it accepts dots instead of commas as decimal delimiter csv to result Converts csv files into outc files The following convention for the must be fulfilled 1 There must be one head line containing variable names not longer than twelve characters 2 The variable names in the head line may contain a box number in paren thesis e g N1p 12 If no box number is contained the box number 1 will be applied automatically 3 The first column may contain time information This time information must consist of equidistant samples The according variable name in the head line must be time or t 4 All variables must have the same number of samples csv to data Converts csv files into _csv symb files The resulting files have the structure of symb fil
17. fixes will work on the last the actual graph only again pretty y axis After pressing pretty y axis all graphs in the drawing area get a scaling on the y axis that matches to round nice numbers Such if the maximum of the displayed variable is f e 8 41 activating pretty y axis results in a scaling to an axis of 9 0 Otherwise there will be an exact scaling to 8 41 smooth If smooth is active the data points will be spline interpolated otherwise they will be displayed as a polygon direct apply If direct apply is active all clicks in the box selector or the variable selector as well as all actions on the different sliders will be immediately evaluated If direct apply is not active the actual settings also creation of new sets or graphs will be evaluated when the button Apply is pressed Such it is possible to prepare more complex displays in a kind of offline mode and get the results displayed in one evaluation same y axis After pressing same y axis all graphs in the drawing area get the same scaling on the y axis This is useful if the same variable is drawn for different boxes The global scaling stays active until same y axis is pressed y axis maximum y axis minimum If only a limited range of values shall be displayed this range can be input manually in the text areas below the labels The values become active after pressing ENTER If no values are filled in the maximu
18. last graph becomes active again This button becomes active after pressing new graph or if two or more graphs are displayed in the drawing area It becomes inactive after pressing erase all graphs or if only one active graph remains in the drawing area erase all graphs This button erases all graphs with all their sets This is useful to clear up the drawing area if you are loosing the overview fix variables The variable selector will become inactive and the present selection of variables will be fixed for the next actions After selecting a new box the plot will display the fixed variables for the selected box Clicking again on fix variables deactivates this mode and the variable selector becomes active again If new graph is pressed whilst fix variables is active all information is piped from the previous graph to the new one except the box numbers which are replaced by the next selected one Chapter 11 The Phase Tool MoViE User s Manual August 26 2012 fix boxes The box selector will become inactive and the present selection of boxes will be fixed for the next actions After selecting a new variable the plot will display the selected variable for the fixed boxes Clicking again on fix boxes deactivates this mode and the box selector becomes active again If new graph is pressed whilst fix boxes is active all information is piped from the previous graph to the new one except the variable name which
19. spaces In J Multivar Anal 38 1991 S 1 14 NetCDF 1997 Rew R Davis G EMMERSON S DAVIES H NetCDF User s Guide for C Version 3 Unidata Program Center 1997
20. well as all actions on the different sliders will be immediately evaluated If direct apply is not active the actual settings also creation of new sets or graphs will be evaluated when the button Apply is pressed Such it is possible to prepare more complex displays in a kind of offline mode and get the results displayed in one evaluation MoViE User s Manual August 26 2012 Chapter 5 The Overview Tool same y axis After pressing same y axis all graphs in the drawing area get the same scaling on the y axis This is useful if the same variable is drawn for different boxes The global scaling stays active until same y axis is pressed y axis maximum y axis minimum If only a limited range of values shall be displayed this range can be input manually in the text areas below the labels The values become active after pressing ENTER If no values are filled in the maximum resp minimum from the data to be displayed will be taken into account If only first graph is active the settings of minimum and maximum will only take effect on the first graph Barchart The data will be displayed as barcharts instead of lines Analysis See chapter 15 command See chapter PS print A PostScript output to an external file will be produced The output files are named mov x ps and can be found in the directory working directory gt plots During a MoViE session the number x is increased
21. OAT X 2 time dim The setting time dim ensures the coupling of the variables to the simulation time stored in time The approach of storing each variable box combination as one NetCDF vari able keeps the CEMoS capabilities of selecting fit to interest sets of store variables instead of storing a variable for all boxes NetCDF files are containing the same amount of information as the outc files Information about the content of an nc file can be shown by typing the command ncdump filename in a terminal window Information about the usage of that program will be displayed by simply typing ncdump Note The nc file format is mainly used to port CEMOS results to other environments The special functions Fourier transformation converting to csv etc of the Prepare Tool see section I4 are actually working with the outc resp outb format only Note The access to variables in NetCDF files works case sensitive on their names such when working with a mix of nc and outc files it will be neccesary to switch to case sensitive handling of results see 3 2 This au tomatically happens when an nc file is loaded on start of MoViE 17 4 xxx symb MoViE User s Manual August 26 2012 17 4 xxx symb The files with the symb extension are holding validation data for model vari ables see chapter 6 Each set of validation data consists of minimum two lines with an identical number of columns The lines contain
22. Tiger Graphics 4 MoViE Model Visualization Environment Version 4 1 User s Manual F Hamberg amp C Kohlmeier August 26 2012 MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Contents C O N cr D et nn 1 Introductio 5 Installation of TigerPack 7 T 13 17 23 31 37 41 47 53 59 63 67 n 75 79 Contents MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 1 Introduction 1 Introduction License The model visualization environment MoViE is part of TigerGraphics TigerPack and was developed to simplify the model analysis of complex mod els The philosophy of MoViE is to allow only reasonable actions and adapts itself to the loaded resultfiles Thus there is no need to remember f e the names of stored variables MoViE adapts the graphical user interface dynamically to the loaded result files MoViE is mainly adapted to the needs of box or layer models but_it has been also successfully used for several kinds of problems Hamberg 1099 For the model development TigerGraphics provides CEMoS A detailed description of using CEMoS and the implementation of complex models under MoViE is modular thus a lot of common functions are used by all tools Nevertheless those common functions are described with each tool to keep the description understandable and readable when only one tool is of actual interest This program is free software you
23. a extractions and saves time when working on large simulation results After data extraction and preparation for the animation the button Start film is activated Remark The extraction of data takes some more time than in the other tools because data must be extracted for all displayed boxes Remark MoViE makes no check if a variable is stored for all boxes Errors still may occur Remark The name info file 17 6 will be read The full name and the unit of the variable will be printed as title Start film Start film opens a film control window Print Loop Start Resume Stop Step forward Step backward Film speed 10 TE 1 2 3 4 5 6 7 6 9 10 Record to PostScript Snapshot to PostScript Figure 7 3 Film control window of the film tool Loop starts the animation and the film will be repeated until Stop is pressed Start starts the animation The animation stops at the end of the time window Resume continues the animation The animation stops at the end of the time window Stop stops the animation at the actual time The Step forward and Step backward buttons allow single step ani mations within the selected time window If the check button Print is active every picture is also stored in a separate PostScript file The output files are named automatically mov_x ps and can be found in the directory lt working directory gt plots MoViE User s Manual August 26 2012 Chapter 7
24. abels titles and legends Additionally it has several features for further statistical analysis and output formats Set Label Additional text can be added to the plot in different fontsizes The text must be given in the text field After confirming this by ENTER the text appears in the drawing area It can be moved by pressing the left mouse button on it and moving the mouse holding the button pressed After releasing the mouse button the title jumps to that position The label can be removed by a right mouse click while holding the shift button pressed The label will appear in the PostScript outputs but not in the xmGrace files http plasma ate weizmann ac il Grace xmGrace is not available for Windows sys 8 tems Chapter 10 The ProfCom Tool MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 11 The Phase Tool 11 The Phase Tool SU Phase Plot for Cetl yel 201 by MoWiE zil3 58 45 48 35 38 25 e 15 16 26 y xC12 7 Figure 11 1 A 3D plot from the phase tool This tool allows the investigation of f e predator prey interactions within the model results 3D plots of variables against each other are possible Chapter 11 The Phase Tool MoViE User s Manual August 26 2012 Phase control panel fix variables 360 J fix ae J scale Set time window 360 a points 5 W direct apply Figure 11 2 Control panel of the pha
25. allation of TigerPack For 3D plots see LI MoViE needs the package Gnuplot is required The current version of MoViE is working with Gnuplot 3 7 patchlevel 3 If Gnuplot is not available only 2D plot are possible in the phase tool Field data that shall be visualized must be stored in a predefined format see 17 The main restriction is that all data must be stored as one dimensional indexed arrays 3Gnuplot is part of Linux distributions Gnuplot can be obtained from http www gnuplot info 2 5 General operating instructions MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 3 Main MoViE Menu 3 Main MoViE Menu EA Tiger Graphics MoviE 3 2 verview Compare Film B Profile ProfCom Phase Contour Prepare License Figure 3 1 Main MoViE menu i bna Pad The main menu contains the following buttons e Overview 2D timeplots of one or more variables and boxes described in chapter 5 e Compare comparing of different simulation results and comparing of results with measured data 6 e Film animation of a selected variable within some predefined maps 7 e Text comparing of different simulation results via numerical output e Profile profile plot where the values are plotted over all boxes resp layers for a specific time step 9 e ProfCom profile plot with the capability of comparing different files and displaying measured data 10 e Phase 2D phase p
26. an man ase oz ec om me pm mn ps ae n ven re pon pp az m Figure 4 1 A sample of a variable selector The variable selector contains a button for every variable stored in the selected result file A variable can be selected by clicking the button via left mouse click The default variable is the variable on the first button If a variable is selected which has not been stored for the given box a message appears in the info window The color for a button can be set in the file name info see 17 6 In this file additional informations for the variable such as units which is displayed in the plot can be set An alternative variable selector nice selector which contains other names in stead of variable names can be constructed By default a file named nicevar info is read if available see 17 7 The normal variable selector and the nice selector can be toggled by clicking the right mouse button in the control panel of any tool If another nicevar file has been loaded by Load NVS it is necessary to toogle again for activating it 4 3 The box selector Overview Compare Text Phase MoViE User s Manual August 26 2012 HFIEFIHH moss nne e BEEPER EEE Figure 4 2 A sample of a box selector 4 3 The box selector Overview Compare Text Phase The box selector contains a button for every box stored in the selected result file A box will be selected by clicking the button The default box is t
27. ated By default is all loaded data sets are activated The activated sets are shown to gether with the model results in the plot window if measured data are available for the selected variable box combination The data must have the structure defined in 17 4 MoViE doesn t distinguish data for different years MoViE User s Manual August 26 2012 Chapter 10 The ProfCom Tool exact When activated and if validation is active measured data are only dis played if they are available for the exact point in time given by the time slider By default Exact is deactivated such all available measured data are displayed Data time window If a value is entered and confirmed by ENTER and exact is activated mea sured data are shown for the given time window with the point in time given by the time slider centered in the time window This is useful if measured data are sparse If no value is given here it defaults to 1 new graph This button activates a new graph This button is redundant The same action can be activated by a right mouse click on the variable box You may have up to nine graphs on in the drawing area which will be auto matically arranged erase graph This button erases the actual graph with all its sets The new last graph becomes active again This button becomes active after pressing new graph or if two or more graphs are displayed in the drawing area It becomes inactive after pressing
28. ble than n1p or n1P It may be useful to have an automatic transformation of variable name to lower case by MoViE Remark This will not effect any data in the result files or data files Font settings During the work with MoViE it turned out that two font sizes must be adjustable These are Button font size Here the font size for the variable selector and the box selector can be defined The two given values allow an adjustment and keep a readable representation for all screen resolutions Plot font size Here three font size for the texts in graphical outputs can be defined There are settings for three different display variants normal The here selected font is used for the legends and the axes when display ing one or two graphs in the plotting window of MoViE small The here selected font is used for the legends and the axes when display ing three or four graphs in the plotting window of MoViE 13 3 Tool control MoViE User s Manual August 26 2012 tiny The here selected font is used for the legends and the axes when display ing five to nine graphs in the plotting window of MoViE Remark The Plot font size has an effect on Postscript outputs but not on xmGrace outputs X axis representation When selected Days the time axis will get ticks and tick labels with months and years It is assumed that a year consists of twelve months with each thirty days The normal setting is numbers 13 3
29. can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Soft ware Foundation either version 3 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABIL ITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this program If not see jhttp www gnu org licenses Chapter 1 Introduction MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 2 Installation of TigerPack 2 Installation of TigerPack TigerGraphics TigerPack is written for UNIX or EAA It will also run on Mac OSX Windows user may use it within a virtual machine TigerPack consists of 4 parts e CEMOS core system for the simulation e CEMTK optional but highly recommended GUI for CEMoS e CEvoS system for evolutionary parameter adaptation for CEMoS models e MoViE visualization package CEMTK and CEvoS can only be used if CEMOS is installed MoViE can be used for any result files with appropriate format 2 1 Requirements All part of TigerPack needs e csh tcsh or bash e gcc 2 6 3 or higher e make e Ta TK optional it is recommended to install e kwrite or gedit gdb with ddd or insight e grace e gv e gnuplot e kdi
30. e all graphs You may have up to 9 sets per graph erase set This button erases the actual the last set from the actual graph After this the new last set of the actual graph becomes active again new graph This button activates a new graph This button is redundant The same action can be activated by a right mouse click on the variable box You may have up to nine graphs on in the drawing area which will be auto matically arranged erase graph This button erases the actual graph with all its sets The new last graph becomes active again This button becomes active after pressing new graph or if two or more graphs are displayed in the drawing area It becomes inactive after pressing erase all graphs or if only one active graph remains in the drawing area erase all graphs This button erases all graphs with all their sets This is useful to clear up the drawing area if you are loosing the overview fix variables The variable selector will become inactive and the present selection of variables will be fixed for the next actions After selecting a new box the plot will display the fixed variables for the selected box Clicking again on fix variables deactivates this mode and the variable selector becomes active again If new graph is pressed whilst fix variables is active all information is piped from the previous graph to the new one except the box numbers which are replaced by the next sel
31. e selector as well as all actions on the different sliders will be immediately evaluated If direct apply is not active the actual settings also creation of new sets or graphs will be evaluated when the button Apply is pressed Such it is possible to prepare more complex displays in a kind of offline mode and get the results displayed in one evaluation Analysis See chapter 15 command See chapter PS print A PostScript output to an external file will be produced The output files are named mov x ps and can be found in the directory working directory gt plots During a MoViE session the number x is increased Grace print This button acts similar to PS print but instead of sending the screens contents to the printer or storing it as PostScript code into a file it produces an xmGrace sm output with all relevant information for legends and labels and stores it into an external file The output files are named mov_x agr and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased xmGrace allows the free arrangement of graphs the modification of colours and linestyles tick marks and tick labels titles and legends Additionally it has several features for further statistical analysis and output formats http plasma ate weizmann ac il Grace xmGrace is not available for Windows Sys 8 tems Chapter 9 The Profile Tool MoViE User s Ma
32. e sets are scaled corresponding to these depths If the variable layer is not stored the results are plotted equidistantly General features of the profile compare tool e up to nine graphs simultaneously not recommended e variation of the simulation time with the time slider The title of the plot shows the names of the variables and the actual time If a file name info exists it will be read The full name and the unit of the variable will be displayed if available The whole data set for all shown layers and all time steps are read if a variable is selected This may take some time especially if only limited memory is available Chapter 10 The ProfCom Tool MoViE User s Manual August 26 2012 Profcom control panel W eval layer _ show layervalue Select startbox A flip y 1 _ same axes 1 7 1319 25 31 Set box window _ Scale to time max 32 axes maximum 1 7 13 19 25 31 axes minimum J validation j exact _ Barchart Data time window j smooth Figure 10 2 Control panel of the Profcom tool Select startbox and Set box window The first displayed box and the numbers of box to follow can be selected If the time window exceeds the maximum number of boxes for startbox the box window will be reduced internally validation Accessible if field data are loaded see 4 1 If more than one data set is loaded a window opens where every data set may be activated or deactiv
33. e will be used instead of the default one 17 7 nicevar info An alternative variable selector nice variable selector which contains other names instead of variable names can be constructed For this a file named MoViE User s Manual August 26 2012 Chapter 17 Data structures nicevar info must be available in the directory where MoViE has been started default Any other name preferably with the extension info is also possible and can be selected by Load NVS These files must have the following structure First line number of columns of buttons in the selector Further lines variables or seperator A line for a variable must have the following structure lt variable name gt lt new name gt lt color gt The color might be any Tcl TK color see man colors Example 2 irr Irradiance navyblue temp Temperature navyblue chl Chlorophyll seagreen zoo Zooplankton seagreen The normal variable selector and the nice selector can be toggled by clicking the right mouse button in the control panel of any tool 17 8 tkmoviedefaults The file is located in the home directory an in addition in the actual model directory It contains the settings of the custom tool 13 It is written if the settings of the custom tool are applied If the file exists in the actual model directory this one will be evaluated otherwise the file from the home directory If no tkmoviedefaults is available the MoViE defaults will be s
34. ected one Chapter 5 The Overview Tool MoViE User s Manual August 26 2012 fix boxes The box selector will become inactive and the present selection of boxes will be fixed for the next actions After selecting a new variable the plot will display the selected variable for the fixed boxes Clicking again on fix boxes deactivates this mode and the box selector becomes active again If new graph is pressed whilst fix boxes is active all information is piped from the previous graph to the new one except the variable name which are replaced by the next selected one act on all graphs This button becomes active if fix boxes or fix variables is selected If act on all graphs is pressed the fixes in variables or boxes will act on all displayed graphs Pressing act on all graphs again deactivates this option The fixes will work on the last the actual graph only again pretty y axis After pressing pretty y axis all graphs in the drawing area get a scaling on the y axis that matches to round nice numbers Such if the maximum of the displayed variable is f e 8 41 activating pretty y axis results in a scaling to an axis of 9 0 Otherwise there will be an exact scaling to 8 41 smooth If smooth is active the data points will be spline interpolated otherwise they will be displayed as a polygon direct apply If direct apply is active all clicks in the box selector or the variable selector as
35. er is followed by a set of nvars strings of each 80 twelve in xxx outb ASCII characters These strings are containing the name of a variable and the box number for which it is stored f e p1c 137 indicates plc of box 137 being stored 17 1 xxx outb and xxx outc MoViE User s Manual August 26 2012 10 After this block of strings which may be some ten kilobytes long the numerical output of the simulation is stored as follows One float is stored in binary format for each variable box combination appearing in the string block 9 One block is stored for simulation times between start 2 and endtim 3 that are multiples of outdelt 5 This block may have a length of several megabytes MoViE User s Manual August 26 2012 Chapter 17 Data structures 17 2 xxx pk outb and xxx pk outc Files with an extension pk outb are holding spectral values from Fourier an alyzed result files see I4 The _pk outc file starts with structural information given in different formats total number of stored variables nvars automatically derived by CE MoS start time of the stored data end time of the stored data number of base vectors one base vector means one data pair for each harmonic as calculated by the Fourier transformation outdelt for synthesizing the data number of cycles the Fourier transformation was calculated for length of the basic cycle length of the first harmonic 1 is stored as unsigned integer 2
36. es Chapter 14 The Prepare Tool MoViE User s Manual August 26 2012 result to data Converts outc files into symb files data to zero outc Converts a symb files into a special _zero outc file The resulting file con tains all variables defined in the symb The values are all set to zero This file is useful if only the data should be visualized data to outc Converts a symb files into a _symb outc file The resulting file contains all variables defined in the symb The values are linearily interpolated A popup window asks for startime endtime outdelt and cycle If the intervall of the resultfile exceeds the data the values for the missing time stamps at the beginning and at the end are set to 9999 0 Distance Files Calculates the pointwise distance of two files The distances of filei outc and file2 outc are stored in a new file named fileli file2 m1 outc Remark The two file must be stored with the same outdelt MoViE User s Manual August 26 2012 Chapter 15 analysis 15 analysis This button opens a separate window which holds the functions of the analysis tool Zee I mean over time window running mean 30 0 _ mean over 1 0 _j sum over ji 0 _j L2 distances Figure 15 1 Analysis control panel HL AM N The next selected variable is added multiplied to the previous resp the previous is divided by the selected one If new set or new graph has been pr
37. essed before the result will appear in the next set resp graph If you like to add f e x 10 x 20 press x in the variable selec tor then press 10 in the box selector press now and then 20 in the box selector It is not possible to add f e x 10 4 y 20 1 P WM A factor may be specified and confirmed by return If then is pressed the next variable will be multiplied divided by Chapter 15 analysis MoViE User s Manual August 26 2012 this factor Attention Do not forget to confirm the factor by ENTER Remark The operations may be combined e and M may be pressed immediately after another then the next selected variable is first multiplied and then added to the previous one Division by zero causes a wave error which doesn t affect the ses sion The numbers divided by zero won t change This may result in misleading plots mean over time window The mean over the adjusted time window Select starttime and Set time window is displayed as one barchart for each selected variable All other features are still active in this mode The mean over time window mode is active as long as the radio button is marked red When used in the text tool see B this function also calculates some more statistical values median maximun minimun stan dard deviation etc running mean The running mean over the selected time window is displayed for each selec
38. esses are evaluated to compose the plot of the profile If the variable layer is not stored or if eval layer is not activated all layer thicknesses are assumed to be equal and constant MoViE User s Manual August 26 2012 Chapter 12 The Contour Tool show layer value If show layer value is selected and if the result file contains information on the layer thickness stored in the variable layer the information on time changing layer thicknesses are evaluated and the depth starting from top is displayed on the layer axis instead of the layer number mark zero values If activated zeros are displayed in grey and not in a color of the color table Color table Opens a menu with different color tables which can be selected Set minimum and Set maximum These buttons affect the color scaling By default the minimum and maximum values are taken over the whole stored simulation time for the selected boxes scheme lower or upper In the text fields the minimum and maximum values may be set by hand All values above the maximum below the minimum are drawn in the maximum minimum color direct apply If direct apply is active all clicks in the box selector or the variable selector as well as all actions on the different sliders will be immediately evaluated If direct apply is not active the actual settings also creation of new sets or graphs will be evaluated when the button Apply is pressed Suc
39. et 17 9 tkmoviemcf This file is located in the actual model directory If existing it contains the last commands of the command window These settings will be restored if the command window is opened again 17 10 tkmovieset MoViE User s Manual August 26 2012 17 10 tkmovieset This file should only be created by advanced MoViE users This file must be located in the home directory It may contain default settings for several global MoViE variables The file contains Tel TK code which sets the variable to the specified value The file must not contain any other lines It is allowed to append a Tcl TK comment after a Example of tkmovieset set prettyaxis 0 set sameaxis 1 sets all y axes to the same value by default MoViE User s Manual August 26 2012 References References Hamberg 1996 HAMBERG F CEMoS eine Programmierumge bung zur Simulation komplexer Modelle Fachbereich Mathematik Carl von Ossietzky Universit t Oldenburg Diplomarbeit 1996 URL http www staff uni oldenburg de cora kohlmeier software dpa pdf Hamberg und Kohlmeier 2004 HAMBERG F KOHLMEIER C CEMoS User s manual 2004 URL http www staff uni oldenburg de cora kohlmeier software cemoscemtk pdf http www staff uni oldenburg de cora kohlmeier software cemoscemtk pdf Krug 1991 Krug P The conditional expectation as estimator of normally distributed random variables with values in infinitely dimensional banach
40. ff3 Nautilus Dolphin user should also install e nautilus open terminal Depending on the different properties of the operating systems the binary files are not portable from Intel machines to other architectures CEMOS itself needs it only for the installtion This can also be done manually if Tcl TK is not available 2 2 Installation MoViE User s Manual August 26 2012 2 2 Installation Copy the file tigerpack tar gz to the directory where do you like to install it and where do you have write permissions Extract it by tar xzvf tigerpack tar gz Open a command terminal in the directory TIGERPACK and type the command setup After that logout and login again to set the environmental variables reboot is NOT necessary 2 3 Reinstalling after update If you already have a running TigerPack and you would like to install an update Open a terminal in TIGERPACK and type the command reinstall No need to logout but existing CEMoS models must be recompiled 2 4 Starting MoViE MoViE cab be started from any directory by mov It is convenient to start it from the directory where your simulation results are in 2 5 General operating instructions MoViE needs for best performance all three mouse buttons In the following chapters the term middle mouse click means to press the middle mouse but ton resp left right If not specified a left mouse click is meant MoViE User s Manual August 26 2012 Chapter 2 Inst
41. g a new box the plot will display the fixed variables for the selected box Clicking again on fix variables deactivates this mode and the variable selector becomes active again If new column is pressed whilst fix variables is active all information is piped from the previous column to the new one except the box numbers which are replaced by the next selected one fix boxes The box selector will become inactive and the present selection of boxes will be fixed for the next actions After selecting a new variable the plot will display the selected variable for the fixed boxes Clicking again on fix boxes deactivates this mode and the box selector becomes active again MoViE User s Manual August 26 2012 Chapter 8 The Text Tool If new column is pressed whilst fix boxes is active all information is piped from the previous column to the new one except the variable name which are replaced by the next selected one act on all columns This button becomes active if fix boxes or fix variables is selected If act on all columns is pressed the fixes in variables or boxes will act on all displayed columns Pressing act on all columns again deactivates this option The fixes will work on the last the actual column only again direct apply If direct apply is active all clicks in the box selector or the variable selector as well as all actions on the different sliders will be immediately evaluated If di
42. gle button 1 9 represents one graph MoViE User s Manual August 26 2012 Chapter 16 command All This button acts differently depending on the selected mode shown in the Recall Store button left of it In the Recall mode this button displays graphs produced by all non empty command lines shown in the text lines below In the Store mode this button stores the sequences that pro duced all visible graphs into the text lines below from where those sequences can be recalled or stored into a file A 19 These buttons act differently depending on the selected mode shown in the Recall Store button above them In the Recall mode these buttons display one graph produced by the command line shown in the text line right of it Normally the last the actual graph is replaced by a graph built by the sequence of commands shown in the text line If new graph has been pressed before a new graph is produced with those commands In the Store mode these buttons store the sequence of the actual graph into the text line at the right from where the sequence can be recalled Advanced user may also edit the command lines In this case only the limited cabability concerning the calculus of MoViE is allowed Remark In some tools only the first set resp graph of the commands will be evaluated Chapter 16 command MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 17 Da
43. h it is possible to prepare more complex displays in a kind of offline mode and get the results displayed in one evaluation Analysis See chapter command See chapter Chapter 12 The Contour Tool MoViE User s Manual August 26 2012 PS print A PostScript output to an external file will be produced The output files are named mov_x ps and can be found in the directory lt working directory gt plots During aMoViE session the number x is increased MoViE User s Manual August 26 2012 Chapter 13 The Custom Tool 13 The Custom Tool gt Tiger Graphics Custom Tool Figure 13 1 Custom tool The Custom tools serves to set some defaults for easier work with MoViE It reads information from one central MoViE resource file tkmoviedefaults which is located in the user s home directory If a file tkmoviedefaults also exists in a model directory it will read instead of the one in the home directory see 17 8 13 1 File selections MoViE User s Manual August 26 2012 13 1 File selections General functions Search opens a file selection dialog where files can be selected Empty removes an entry from the setting under regard Entries in the text fields can be made by keyboard as well They have to be comfirmed by pressing ENTER The following preselections are possible Default result file 2 and Default result file 3 When setting up new models it might be convenient to
44. have automatic access to previously prepared standard simulation results for comparison The here selected files are available for the Compare tool see 6 1 the text tool see 8 the ProfCom tool see without reloading them when starting MoViE for new Default Data Directory Here the path to the top level directory can be set where measured data are stored Default data file 1 to Default data file 5 Here a set of data files with measured data compare can be preselected for model evaluation These files don t need to be in the path as set in Default Data Directory but the Search starts at point in the directory tree The here selected files are available for the Compare tool see 6 1 the text tool see B the ProfCom tool see 10 without reloading them when starting MoViE for new MoViE User s Manual August 26 2012 Chapter 13 The Custom Tool 13 2 Other settings Screen settings The appearance of MoViE can be adjusted to the available resolution of the screen Due to the fact that plot window and the text window for numerical output need the most space the appearance is controlled by the canvas size The canvas size can be optimized in five steps for screen resolutions from 600 800 to 1280 1024 pixels Case sensitive result files When selecting case sensitive result files MoViE will distinguish variable according to the case of characters E g Nip will be handled as a different varia
45. he box on the first button If a variable box combination is selected which has not been stored in the result file a message appears in the info window If a box is selected which has not been stored for the given variable a message appears in the info window See also figure 4 2 4 4 The Time slider Profile Profcom 105 00 140 00 175 00 210 00 245 00 280 00 315 00 from 0 000000 to 360 000000 Record to Postscript Figure 4 3 A sample of the time slider The actual time for the plot can be modified by the time slider A range in time can be input manually in the text areas below the time slider The values become active after pressing ENTER The values in these text areas are delimiting the range in time for the sequence Postscript outputs which can be produced by pressing the button Record to Postscript Remark Every time the slider is set to the start time left the results will be extracted for the complete time interval This may take some time MoViE User s Manual August 26 2012 Chapter 5 The Overview Tool 5 The Overview Tool 110 23 V Nitrate N n Box8 mmol m3 F bi EIE aoe a 12 78 Be Nate nan Sube sa 91 86 Diatoms Pic Box15 rmgC m3 10 33 zu 73 49 Fat 7 67 IN 5542 F N p 5 11 yo P 36 74 F i poy 3 VA 2 56 3 18 37 N E dd A Wm sus my s 0 00 pe ee 0 00 gee ee
46. he connect mode is now active until the button disconnect sliders is pressed This is the configuration at start of the tool multiple sets If activated more than one set can be selected If only one result file is loaded the compare tool behaves similar to the overview tool If more than one result file is loaded the sets for the different results are distinguished by different line thicknesses while the different sets are distinguished by different colors This may be sometimes a little bit confusing Activating multiple sets activates the controls for new set erase set and erase all sets MoViE User s Manual August 26 2012 Chapter 6 The Compare Tool validation Accessible if field data are loaded see K I If more than one data set is loaded a window opens where every data set may be activated or deactivated By default is all loaded data sets are activated The activated sets are shown to gether with the model results in the plot window if measured data are available for the selected variable box combination The data must have the structure defined in MoViE doesn t distinguish data for different years number of harmonics If one loaded result file is a pk file 17 1 this button appears The number of harmonics can be selected where O means that for all loaded pk files all available harmonics are evaluated default The maximum number which can be selected manually is the smallest number of harmonics ava
47. ilable for all loaded pk files new set This button activates the next plot line set The same action can be activated by a middle mouse click on the variable box This new set remains active for all actions f e from analysis until another set is activated new set or left mouse click onto a vari able box it is erased erase set or right mouse click onto the set a new graph is activated new graph or right mouse click onto a variable box the actual graph is erased erase graph all graphs are erased erase all graphs You may have up to 9 sets per graph erase set This button erases the actual the last set from the actual graph After this the new last set of the actual graph becomes active again Chapter 6 The Compare Tool MoViE User s Manual August 26 2012 new graph This button activates a new graph This button is redundant The same action can be activated by a right mouse click on the variable box You may have up to nine graphs on in the drawing area which will be auto matically arranged erase graph This button erases the actual graph with all its sets The new last graph becomes active again This button becomes active after pressing new graph or if two or more graphs are displayed in the drawing area It becomes inactive after pressing erase all graphs or if only one active graph remains in the drawing area erase all graphs This button erases a
48. it produces an xmGrace D output with all relevant information for legends and labels and stores it into an external file The output files are named mov x agr and can be found in the directory working directory gt plots During a MoViE session the number x is increased xmGrace allows the free arrangement of graphs the modification of colours and linestyles tick marks and tick labels titles and legends Additionally it has several features for further statistical analysis and output formats Set Label Additional text can be added to the plot in different fontsizes The text must be given in the text field After confirming this by ENTER the text appears in the drawing area It can be moved by pressing the left mouse button on it and moving the mouse holding the button pressed After releasing the mouse button the title jumps to that position The label can be removed by a right mouse click while holding the shift button pressed The label will appear in the PostScript outputs but not in the xmGrace files Ihttp plasma ate weizmann ac il Grace xmGrace is not available for Windows Sys 8 tems Chapter 11 The Phase Tool MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 12 The Contour Tool 12 The Contour Tool 0 14 3803 Figure 12 1 A snapshot from the Contour tool The Contour Tool is a more specialized tool to work with simulation results from layer oriented models It gives a
49. ll graphs with all their sets This is useful to clear up the drawing area if you are loosing the overview fix variables The variable selector will become inactive and the present selection of variables will be fixed for the next actions After selecting a new box the plot will display the fixed variables for the selected box Clicking again on fix variables deactivates this mode and the variable selector becomes active again If new graph is pressed whilst fix variables is active all information is piped from the previous graph to the new one except the box numbers which are replaced by the next selected one fix boxes The box selector will become inactive and the present selection of boxes will be fixed for the next actions After selecting a new variable the plot will display the selected variable for the fixed boxes Clicking again on fix boxes deactivates this mode and the box selector becomes active again If new graph is pressed whilst fix boxes is active all information is piped from the previous graph to the new one except the variable name which are replaced by the next selected one MoViE User s Manual August 26 2012 Chapter 6 The Compare Tool act on all graphs This button becomes active if fix boxes or fix variables is selected If act on all graphs is pressed the fixes in variables or boxes will act on all displayed graphs Pressing act on all graphs again deactivates this option The
50. lots of 2 selected variables described in chapter 11 e Contour Contour plot Displaying values for all time steps and boxes resp layers The values are encoded by colors 12 e Custom Custom Tool Customize MoViE for the special needs of users by settings fonts paths etc 13 Chapter 3 Main MoViE Menu MoViE User s Manual August 26 2012 e Prepare Prepare Tool Transformation of simulation results to differ ent formats Fourier transformation of simulation results and measured data Import and export filters See 14 e License License Clicking on Exit closes the MoViE session MoViE User s Manual August 26 2012 Chapter 4 Main Control 4 Main Control The MoViE tools are controlled in a similar way The control instances affecting nearly all tools are described here Every tool consists of the main window where the output is plotted and some control buttons 4 1 Main control buttons Load Result File Overview Film Profile Phase Contour A file selector window appears which shows all result files in the working di rectory A result file can be selected by left mouse click and confirmed by OK The loading procedure will take some time depending on the size of the result file After loading the file selector box disappears and a message appears in the info window _pk oute containing spectrum data made by MoViE may be also loaded MoViE recognizes automatically if the file contains Fo
51. m resp minimum from the data to be displayed will be taken into account Chapter 6 The Compare Tool MoViE User s Manual August 26 2012 If only first graph is active the settings of minimum and maximum will only take effect on the first graph Barchart The data will be displayed as barcharts instead of lines Analysis See chapter 15 command See chapter PS print A PostScript output to an external file will be produced The output files are named mov x ps and can be found in the directory working directory gt plots During a MoViE session the number x is increased Grace print This button acts similar to PS print but instead of sending the screens contents to the printer or storing it as PostScript code into a file it produces an xmGrace im output with all relevant information for legends and labels and stores it into an external file The output files are named mov_x agr and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased xmGrace allows the free arrangement of graphs the modification of colours and linestyles tick marks and tick labels titles and legends Additionally it has several features for further statistical analysis and output formats Set Label Additional text can be added to the plot in different fontsizes The text must be given in the text field After confirming this by ENTER the text appears in Iht
52. n overview on the complete development of concentrations and layer thicknesses over a time window The time infor mation is given on the x axis the layer thickness information is given on the y axis starting from top and the concentration of the displayed variable is coded by color To adjust the different axes to the region of interest the following controls are implemented Chapter 12 The Contour Tool MoViE User s Manual August 26 2012 Contour control panel W eval layer 0 360 _ show layervalue ps W mark zero values Set time window 360 Color table Maximum value 5 360 Minimum value nel W direct apply 1 7 13 19 25 31 Apply Set box window 5 Analysis EI Command 0 6 12 18 24 30 PS print Figure 12 2 Control panel of the Contour tool Select starttime and Set time window The starting time of the plot and the period which shall be plotted can be selected If the time window exceeds the endtime for a starttime the time window will be reduced accordingly Select startbox and Set box window The first displayed box and the numbers of box to follow can be selected If the time window exceeds the maximum number of boxes for startbox the box window will be reduced internally eval layer If eval layer is selected and if the result file contains information on the layer thickness stored in the variable layer the information on time changing layer thickn
53. nges during simulation Compare control panel The control panel contains all buttons and sliders for modifying the actual plot and the plotting mode Select starttime and Set time window The starting time of the plot can be selected independently for every result file with Select starttime 1 Select starttime 2 and Select starttime 3 The time window can be set with the common Set time window slider If Chapter 6 The Compare Tool MoViE User s Manual August 26 2012 o 360 1 fix variables po 1 fix boxes Select starttime Ei o a pretty y axis 0 360 j same y axis Set time window y axis max 360 E ji y axis min only first graph W connect sliders j smooth multiple sets 4 validation Foe MENSES X direct apply WE show bars new set Analysis erase s Command erase all sets PS print Grace print new graph Set Label erase all grap Figure 6 2 Control panel of the compare tool the time window exceeds the endtime for a starttime the time window will be reduced The starttime can be set for all result files in common by connect sliders connect sliders disconnect sliders If the starttime for all graphs shall be the same the connect sliders shall be pressed Now all graphs get the starttime given by Select starttime 1 The other starttime sliders will be deactivated and the name of the button changes to disconnect sliders T
54. nimation 7 1 The control panel MoViE User s Manual August 26 2012 Control panel Iof x Select starttime 0 _j show borderlines H _ show box numbers ark al oo im zero values Set time window Bn scd 353 Tracer 1 choose map S ML Set minimum value TS Set maximum value Figure 7 2 Control panel of the film tool Select starttime and Set time window The starting time of the plot and the period which shall be plotted can be selected If the time window exceeds the endtime for a starttime the time window will be reduced accordingly Upper Boxes Lower Boxes The name of the button shows the selected layer of boxes Due to the box set up surface or sediment boxes can be animated The button activates apply Set minimum and Set maximum These buttons affect the color scaling By default the minimum and maximum values are taken over the whole stored simulation time for the selected boxes scheme lower or upper In the text fields the minimum and maximum values may be set by hand All values above the maximum below the minimum are drawn in the maximum minimum color The use of this is given if f e the abundance of phytoplankton during winter shall be investigated The calculation of the maximum over a whole year leads to a very high dynamics during the spring bloom Such there will be no color contrast during winter MoViE User s Manual August 26 2012 Chapter 7 The Film Tool
55. nual August 26 2012 Set Label Additional text can be added to the plot in different fontsizes The text must be given in the text field After confirming this by ENTER the text appears in the drawing area It can be moved by pressing the left mouse button on it and moving the mouse holding the button pressed After releasing the mouse button the title jumps to that position The label can be removed by a right mouse click while holding the shift button pressed The label will appear in the PostScript outputs but not in the xmGrace files MoViE User s Manual August 26 2012 Chapter 10 The ProfCom Tool 10 The ProfCom Tool cms Time 230 pio le_d Figure 10 1 A snapshot from the Profcom tool This tool allows a close look to the change of concentration in different layers It combines the capabilities of the Compare Tool see 6 and the Profile Tool see 9 Extended use of measured data is possible by a lot of control functions Here the typical box structure is interpreted as layer structure Every variable must be stored for a continuous set of layers boxes The concentration is displayed on the x axis for every layer starting on top with the layer with the smallest number If a variable named layer is stored for a continuous set of box numbers those values are interpreted as thickness of the corresponding layer These layer in formation may vary in time So dynamically adapted layer thicknesses can be visualized Th
56. rect apply is not active the actual settings also creation of new columns will be evaluated when the button Apply is pressed Such it is possible to prepare more complex displays in a kind of offline mode and get the results displayed in one evaluation Analysis See chapter command print Exit See chapter An ASCII output will be produced containing exactly the information as dis played in the text window The output files are named mov_x asc and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased Leaves the tool and activates the main menu Chapter 8 The Text Tool MoViE User s Manual August 26 2012 Arrange Windows The variable selector the box selector and the control panel will be arranged on top The Info Window AII informations and errors will be displayed here MoViE User s Manual August 26 2012 Chapter 9 The Profile Tool 9 The Profile Tool nh Time 160 m3 Time 160 1 po4 Time 150 Figure 9 1 A plot from the profile tool This tool allows a close look to the change of concentration in different layers Here the typical box structure is interpreted as layer structure Every variable must be stored for a continuous set of layers boxes The concentration is displayed on the x axis for every layer starting on top with the layer with the smallest number If a variable named layer is stored for a contin
57. s have already been loaded within another tool they will be reloaded in the actual tool Load Data Compare Profcom A file select window appears which contains buttons for loading data files After pressing the button a selector window appears which shows all data files symb files in the default validation directory see 13 or in the working directory if no default is set A file can be selected by mouse click and confirmed by OK If further data files shall be loaded Load Results has to be pressed again Load NVS A file select window appears which contains buttons for loading nicevar files to customize the variable selector see 4 2 After pressing the button a selec tor window appears which shows all files with extension info in the working directory A file can be selected by mouse click and confirmed by OK Attention You have to keep care by yourself that the info file has the right structure see 17 7 View all tools The control panel the variable selector the box selector resp time slider appear and the first available variable is selected Exit Leaves the tool and activates the main menu MoViE User s Manual August 26 2012 Chapter 4 Main Control Arrange Windows The variable selector the box selector and the control panel will be arranged on top The Info Window All informations and errors will be displayed here 4 2 The variable selector all tools u on mn
58. s means that the simulation output is written sequentially although the number of store events is determined by starttime endtime and outdelt variables The following variables are describing the the structure of the nc file similar tol7 1 INC INT varnumber total number of stored variables NC_FLOAT starttime start time of the simulation NC_FLOAT endtime end time of the simulation NC_FLOAT maxdelt maximum timestep of the simulation NC_FLOAT outdelt simulation time between two outputs NC_FLOAT year year where the simulation starts INC FLOAT cycle length of a model s year NC_CHAR model_dir 80 relative path to the main model s direc tory stored as string of 80 ASCII characters NC_FLOAT time time_dim simulation time do reference from the position in the file to the simulation time MoViE User s Manual August 26 2012 Chapter 17 Data structures INC FLOAT proceed this variable holds the actual simulation time of the simulation run when reading results from a still running or from an interrupted simulation When a simulation is finished it holds the same value as endtime All variables are expected as a combination of name box with the same di mensions as time where the NetCDF interface keeps track of the actual stored amount of time steps Such if the variable X should be stored for the boxes 1 and 2 the following shall appear in the nc file NC_FLOAT X 1 time_dim and NC FL
59. se tool The control panel contains all buttons and sliders for modifying the actual plot and the plotting mode Select starttime and Set time window The starting time of the plot and the period which shall be plotted can be selected If the time window exceeds the endtime for a starttime the time window will be reduced accordingly new set This button activates the variable for the y axis The next selected variable is plotted against the previous The same action can be activated by a middle mouse click on the variable box Yet another use of this button resp the next middle mouse click activates the variable for the z axis and the display then shows a 3D plot To control the view angles of the 3D plot a window containing two sliders appears erase set This button erases the actual the last set from the actual graph MoViE User s Manual August 26 2012 Chapter 11 The Phase Tool EE 0 10 20 30 40 50 60 70 80 90 50 0 10 20 30 40 50 60 70 80 90 Figure 11 3 Sliders to control the view angles of a 3D plot After this the new last set is plotted as time plot new graph This button activates a new graph This button is redundant The same action can be activated by a right mouse click on the variable box You may have up to nine graphs on in the drawing area which will be auto matically arranged erase graph This button erases the actual graph with all its sets The new
60. ta structures 17 Data structures 17 1 xxx outb and xxx outc Files with an extension outb or xxx outc are holding model outputs of CE MoS The format xxx outb is the standard SESAME format The format xxx outc is derived from that format and removes the limitation of twelve characters from variable names and the the path to the model directory With the xxx outc the variable names and the path to the model directory may consist of 80 characters each In the following the xxx outc formast is described with the xxx outb values in brackets The 1 outc file starts with structural information given in different formats total number of stored variables nvars automatically derived by CE MoS start time of the simulation start read from cemos par normally 0 for January 1 of year see 6 end time of the simulation endtim read from cemos par maximum timestep of the simulation maxdelt read from cemos par simulation time between two outputs outdelt read from cemos par year where the simulation starts year read from cemos par stored is max 0 year length of a model s year cycle read from cemos par normally 360 days representing 12 months of 30 days 1 is stored as unsigned integer 2 7 are stored as floats in binary format 8 9 relative path to the main model s directory stored as string of 80 twelve in xxx outb ASCII characters read from cemos par This head
61. ted variable The length of the time window can be set in the text window on the right hand side of the label It must be confirmed by ENTER All other features are still active in this mode The running mean mode is active as long as the radio button is marked red mean over The mean over the time window of the given length is displayed for each selected variable The length of the time window can be MoViE User s Manual August 26 2012 Chapter 15 analysis set in the text window on the right hand side of the label It must be confirmed by ENTER All other features are still active in this mode The mean over mode is active as long as the radio button is marked red sum over The sum over the time window of the given length is displayed for each selected variable The length of the time window can be set in the text window on the right hand side of the label It must be confirmed by ENTER All other features are still active in this mode The mean over mode is active as long as the radio button is marked red L2 distances Remark This feature is only active in the environment of the compare tool and if result files with spectrum data are loaded see IA A new selection window appears to select the L2 distances to be calculated The selected L2 distances are calculated and displayed in the output windows of the L2 distance tool close Closes the analysis control window Chapter 15 analysis
62. the time information and the value In addition lines for standard deviation validity range of the value time of day are possible 1st column from the beginning to the first contains the name of the variable and the boxnumber in brackets 2nd column between first and second denotes the meaning of the TOW tim time information as numeric value ymd Time information as days as alternative to tim The format is YYMMDD f e 890815 means August 15 1989 tid Additional row to ymd Indicates the time of day The format is hhmm f e 1430 indicates 2 30 pm val indicates the value s of the measurement s to follow std indicates the standard deviations of the values int inb alternative to std indicate non symmetrical quantiles in stead of the symmetrical standard deviation where int denotes the value above val and inb denotes the value below val to be taken for the error bar in the plot per indicates the length of the interval of validity for val given at ymd 17 5 xxx mcf mcf files contain predefined sets of variables see 16 1 Every line within a file corresponds to a graph Within a line the sets are separated by whitespaces Up to nine lines are possible Empty lines should be marked by empty Example MoViE User s Manual August 26 2012 Chapter 17 Data structures nip 1 nip 2 nip 3 n4n 1 n4n 2 n4n 3 nAn 1 n3n 1 n4n 2 n3n 2 n4n
63. tion about a variable is given in name info the name stored in the simulation result file will be used Chapter 5 The Overview Tool MoViE User s Manual August 26 2012 Overview control panel ta 5 Control panel DI VES _ fix variables i fix boxes 4 all graphs its starttime lm pretty y axis EE gt 0 ggg Same y axis o o y axis max Set time window J 360 y axis min only first graph 1 smooth Barcharts direct apply Figure 5 2 Control panel of the Overview tool The control panel contains all buttons and sliders for modifying the actual plots and the plotting mode Select starttime and Set time window The starting time of the plot and the period which shall be plotted can be selected If the time window exceeds the endtime for a starttime the time window will be reduced accordingly new set This button activates the next plot line set The same action can be activated by a middle mouse click on the variable box This new set remains active for all actions f e from analysis until another set is activated new set or left mouse click onto a vari able box it is erased erase set or right mouse click onto the set a new graph is activated new graph or right mouse click onto a variable box MoViE User s Manual August 26 2012 Chapter 5 The Overview Tool the actual graph is erased erase graph all graphs are erased eras
64. tp plasma gate weizmann ac il Grace xmGrace is not available for Windows sys tems MoViE User s Manual August 26 2012 Chapter 6 The Compare Tool the drawing area It can be moved by pressing the left mouse button on it and moving the mouse holding the button pressed After releasing the mouse button the title jumps to that position The label can be removed by a right mouse click while holding the shift button pressed The label will appear in the PostScript outputs but not in the xmGrace files Chapter 6 The Compare Tool MoViE User s Manual August 26 2012 MoViE User s Manual August 26 2012 Chapter 7 The Film Tool 7 The Film Tool Diatoms Pic mgCAm3 Pe el es er Figure 7 1 A snapshot of an animation This tool allows an animation of a selected variable in a predefined map The animation works highly interactive single pictures different start and end time different color tables and different scalings are possible The definition of a new map requires knowledge in programming Tcl TK The maps have to be adapted to the specific models The capability of the film tool can be seen by loading the default result outc file included in MoViE It is an output file from the 15 box model version of ERSEM Remark This file is automatically loaded if the working directory does not contain a file named result outc 7 1 The control panel The control panel contains all buttons and sliders for preparing the a
65. uous set of box numbers those values are interpreted as thickness of the corresponding layer These layer in formation may vary in time So dynamically adapted layer thicknesses can be visualized The sets are scaled corresponding to these depths If the variable layer is not stored the results are plotted equidistantly General features of the profile tool e up to nine graphs simultaneously not recommended e up to nine variables in one graph The whole data set for all shown layers and all time steps are read if a variable is selected This may take some time especially if only limited memory is available Chapter 9 The Profile Tool MoViE User s Manual August 26 2012 e variation of the simulation time with the time slider The title of the plot shows the names of the variables and the actual time If a file name info exists it will be read The full name and the unit of the variable will be displayed if available Profile control panel Figure 9 2 Control panel of the Profile tool The control panel contains all buttons and sliders for modifying the actual plot and the plotting mode Select startbox and Set box window The first displayed box and the numbers of box to follow can be selected If the time window exceeds the maximum number of boxes for startbox the box window will be reduced internally new set This button activates the next plot line set The same action can be activated by a middle mo
66. urier coefficients in stead of simulation results and directs it into a Fourier synthesis routine If more than one file is loaded only the common variables boxes and time window will be displayed Remark If a file has already been loaded within another tool it will be reloaded in the actual tool Load Results Compare Text Profcom A file select window appears which contains buttons for loading up to five re sult files At start only the first one is loaded the following are empty If more than one result file is loaded the following files may be released with Release all Cancel closes the window Clicking on the buttons opens a file selector window which shows all result files in the working directory A result file can be selected by mouse click and confirmed by OK The loading procedure will take some time depending on the size of the result file After loading the file selector box and the file selector window disappear and a message appears in the info window 4 1 Main control buttons MoViE User s Manual August 26 2012 If further results files shall be loaded Load Results has to be pressed again _pk outc may be also loaded MoViE recognizes automatically if the file contains Fourier coefficient instead of simulation results and directs it into a Fourier synthesis routine If more than one file is loaded only the common set of variables boxes and the commom time window will be displayed Remark If file
67. use click on the variable box MoViE User s Manual August 26 2012 Chapter 9 The Profile Tool This new set remains active for all actions f e from analysis until another set is activated new set or left mouse click onto a vari able box it is erased erase set or right mouse click onto the set a new graph is activated new graph or right mouse click onto a variable box the actual graph is erased erase graph all graphs are erased erase all graphs You may have up to 9 sets per graph erase set This button erases the actual the last set from the actual graph After this the new last set of the actual graph becomes active again new graph This button activates a new graph This button is redundant The same action can be activated by a right mouse click on the variable box You may have up to nine graphs on in the drawing area which will be auto matically arranged erase graph This button erases the actual graph with all its sets The new last graph becomes active again This button becomes active after pressing new graph or if two or more graphs are displayed in the drawing area It becomes inactive after pressing erase all graphs or if only one active graph remains in the drawing area erase all graphs This button erases all graphs with all their sets This is useful to clear up the drawing area if you are loosing the overview Chapter 9 The Profile Tool
68. ve the data points will be spline interpolated otherwise they will be displayed as a polygon direct apply If direct apply is active all clicks in the box selector or the variable selector as well as all actions on the different sliders will be immediately evaluated If direct apply is not active the actual settings also creation of new sets or graphs will be evaluated when the button Apply is pressed Such it is possible to prepare more complex displays in a kind of offline mode and get the results displayed in one evaluation MoViE User s Manual August 26 2012 Chapter 10 The ProfCom Tool Analysis See chapter command See chapter 16 PS print A PostScript output to an external file will be produced The output files are named mov_x ps and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased Grace print This button acts similar to PS print but instead of sending the screens contents to the printer or storing it as PostScript code into a file it produces an xmGrace a output with all relevant information for legends and labels and stores it into an external file The output files are named mov_x agr and can be found in the directory lt working directory gt plots During a MoViE session the number x is increased xmGrace allows the free arrangement of graphs the modification of colours and linestyles tick marks and tick l

User's Manual - Carl von Ossietzky Universität Oldenburg

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User's Manual - Carl von Ossietzky Universit&auml;t Oldenburg

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User's Manual - Carl von Ossietzky Universität Oldenburg