User's manual for Display_MICRESS
Contents
1. microstructure evolution simulation software Display MICRES Version 5 9 October 2007 User s Manu Display MICRESS Introduction Display_MICRESS DP_MICRESS is a post processing tool with a wide span of possibilities ranging from basic display and image output to advanced features such as zooming multiple display build in four folded symmetry animation and Virtual EDX It can also handle several files simultaneously It can read results file in binary single and double precision native or not and ASCII compressed or not as well as perform conversions between these formats Libraries Display MICRESS relies on the following libraries PGPlot www astro caltech edu tip pgplot for all graphical operations PNG www libpng orgl for images output htip www zlib netis used for compression by the PNG library and for compressing files GrWin http spdq1 sci shizuoka ac jp grwinlib english is used as a screen driver for PGPlot under Windows DP_MICRESS the graphical user interface to Display MICRESS is written in Perl www perl org uses extensively the Perl Tk module www ni s u net com and is packed as an executable with PAR par perl org Running Display MICRESS Display MICRESS can be called from a shell providing the name of the result file s to be displayed it does not allow switching between files meaning it shall be restarted to display another file2. level intercept on axis Display_MICRESS Page 9 of 10 Outputs O l Write an Image output of current time step O J Write images output of each time step O L Toggle on and off writing of larger images O H Toggle on and off writing of high resolution images O A Write an ASCII output of current time step O B Write ASCII outputs of each time step O N Switch between time stamp and numbering markers O C Write an image of the colour scale O T Write PNG images with transparent background O 0 Write PNG images with opaque background O G Write GIF Graphics Interchange Format images O P Write post script images O D Accept default names Virtual EDX E D Display virtual EDX scan for current time step E E Same as above for all time steps E C Same as above for a selection of time steps E X Virtual EDX on a line parallel to the X axis E Y Virtual EDX on a line parallel to the Y axis E R Re plot scan line E S Re scan scan line E N Toggle on and off normalising the scans E F Front tracking E P Scan point Virtual EDX outputs R T Text output for current time step R U Text output for all time steps R I Scan position output for current time step R J Scan position output for all time steps R C Image of t
3. It can for example be called with DP_MICRESS Test phas if no argument is provided a summary of command line options is returned Command line options gt b results in binary single precision p divide display in panels row major two gt z read compressed results integers separated by x following p gt 3 4 9 respectively three four or nine ex p2x3 folded symmetry q divide display in panels column major gt f read automatic min max from the first time ex q2X3 step g read run time instructions from standard Min value Max value explicitly specify the input to allow piping from GUI device min and max to use t Transfer MICRESS converts file m multiple results specify the number of Animate animate to the end gt gt result files integer value following m ex m6 automatic min max from the whole file number of panels fits the nb of solutions Help print a list of all available command line options no graphical user interface when called from the command line Multiple display this feature is restricted to results files with the same geometry Compressed files the whole files are decompressed to temporary files which are erased when the program is exited it is therefore preferable to close Display MICRESS nicely i e no interruption to avoid leaving those files in the working directory Non native files Display MICRESS
4. also be colour coded in the traditional way contribution of 001 011 and 111 orientations When these display modes are activated the corresponding colour scale is plotted in a secondary window under Irix and Linux unfortunately not under Windows a separate picture can be written out instead When two results are displayed it is possible to display their difference with D D Display_MICRESS Page 5 of 10 It is possible to use a logarithmic scale DN the result data is first cut off to the maximum and minimum for the scale which should be positive It is also possible to take the absolute value of the results with D A Vector field Display MICRESS also supports vector field representation which can be activated with B 2 the last file displayed being the Y component of the vector and the last but one the X component this is obviously only available with three files at least when more are displayed they get the same vector field Similarly a 3D vector field mode is also available B N the X Y and Z components of the vectors are respectively read from the last three files the two ones in use depending on the cutting plane direction the third one being temporarily ignored The corresponding settings can be modified with B S they are the minimum and maximum intensity to be plotted the thinning distance the averaging area for which a vector is displayed and the position of the vector in this
5. area centred or not A vector scale representing the maximal intensity can be plotted with B X The colour of the vectors can be controlled with B B which loops through black white and bi colour Isolines Display MICRESS supports various isolines options the first of which is their display which can toggled on and off with D Automatic isolines I 1 9 automatically adds the corresponding number of isolines equally spaced on the scale Similarly a user defined number of automatic isolines can be added with I N User defined isolines can be added with I A A single isoline can be removed with I R and all of them with 1 S By default isolines are displayed with the image in the background but this can be toggled on and off with IC With the feature only the contours are displayed i e only the isolines The values of the isolines currently displayed can be printed in the shell with V To ensure that they can easily seen against any background the isolines are by default black and white this can be changed with B bi coloured isolines An ASCII file listing the coordinates of contour points for current time step can be created with I W and for all outputs with IX Note if several result files are displayed the user will be prompted to select the files to which these operations should be applied to Similarly to what is implemented for the scale user defined settings will affect all solutions which are se
6. can handle non native binary results but the necessary on the fly conversion nevertheless takes time converting the files is often a reasonable option It is also impossible to display files with different endian ness Display_MICRESS Page 2 of 10 Transfer MICRESS This tool converts results file to and from the following formats binary both single and double precision and ASCII compressed or not The ASCII format is useful to transfer results between platforms Transfer MICRESS can also rename MICRESS result files using Irix or Windows naming conventions It can for example be called with DP MICRESS t Test Binary phas Test ASCIl phas if no argument apart from t is provided a summary of command line options is returned Command line DP MICRESS t options i Input_File o Output_File i and o can omitted if file names are specified in that order the output name can be omitted altogether if it is the same as the input a input file in ASCII g input is a geoF file gt d input file in double precision w transfer whole set of results gt e input file in binary single precision gt k remove output from result file ex k5 to gt y compressed input file remove fifth output gt b output file in binary single precision gt l remove sequentially from result file ex 15 gt f output file double precision I7to remove 5 and 7 outputs a c output file i
7. of the colour scale can be increased with V T the font size for the comments if any will also be modified at the same time The default background colour is black but can be switched to white with V W which also affects images output Please note that writing transparent PNG images with a white background does not always provide good readability Displaying with thin 1D results i e with a large number of cells can sometimes be a bit dissatisfactory toggling on the enhanced 1D display mode with V 7 usually helps If a TabF result file was written the temperature at the bottom can be displayed with V K Secondary windows can be closed with V X meaning the colour scale virtual EDX and scan point windows Display The display of length scale is toggled on and off by D L the reference length can be set by default or chosen by the user with D M Letting Display MICRESS select the length to be displayed automatically ensures that its representation is between one fifth and half of display By default this scale is horizontal but it can also be flipped to vertical with D F Known limitation the display of the length scale is not satisfactory with high zooming but the results are anyway deemed not have much meaning at the corresponding resolutions The zoom can be called with D Z the user then has to define the zoom box area which will be displayed afterwards by setting two opposite corners with mouse clicks once th
8. the last output F Go to the first output M N Display the next output dissociated M P Go back to the previous output dissociated M L Go to the last output dissociated M F Go to the first output dissociated Scale S M User defined min and max of the scale S R User defined range median value and range S4D Set min and max from display S G Revert to global min and max S F Force re reading of the file to set min and max Colour scale C 1 11 Select the colour scale to be used C L Loop though available colour scales C F Fiddle with the brightness and contrast C R Reset the brightness and contrast C Invert the colour scale C C Cut off the min and max C S Stepwise colour scale C U User defined steps for stepwise colour scale C T Toggle between user defined and default steps C K Random stepwise colour scale Animation A R Run animation A E Animate to the end A S Modify animation settings Display_MICRESS Page 8 of 10 View V P Reset number of panels V F Freeze panel V R Redraw V Q Auto replot V S Resize V Z Auto resize V A Display annotations V C Display the colour scale in a secondary window V 0 Change the orientation of the annotations V T Increase thickness of the colour scale V W Change the
9. IF Display_MICRESS Page 6 of 10 Graphics Interchange Format with O G or PostScript with O P Changing the image driver affects both images and Virtual EDX outputs The writing of PNG images is unfortunately not available under Windows where the default image driver is GIF The default names can be automatically accepted with O D Virtual EDX The Virtual EDX tool scans any given line from the display and plots the variation of the field variable along this line It can be called by E D after which the user is to set the beginning and end of the scan line with two mouse Clicks similarly to what is implemented for the zoom tool the selected line is displayed on screen and can be refused by pressing the right mouse button or X in which case another line can be set or accepted by pressing any other key The results of the scan are then displayed in a secondary window It is also possible to display in a single plot the scans along the selected line for all time steps with E E or for a selection of outputs with E C chosen time steps It is also possible to select lines parallel to the X or Y axis of the display respectively with EX and E Y the user can specify the line by entering the coordinate of the cut similarly to what the LineScan tool does The last selected scan line can be plotted again with E R replot or re scanned with E S Scans can be normalised rescaled so that their integral is one with E N
10. V P this should be self explanatory The display can be restricted to a given panel with Freeze panel V F this option is only available when a single result file is displayed all subsequent display will be made in the corresponding panel This feature is convenient to visualise in the same window specific outputs from a simulation A secondary window is open displaying the current panel setting clicking on one panel selects it and a second click validates the selection Redraw V R which can be useful when the user wants to update the display for example after changing some display parameter An auto replot feature is also available with V Q Resize V S makes Display MICRESS take into account the possible resizing of the display window made by the user and updates the viewport accordingly An auto resize feature can also be switched on and off with V Z Displaying annotations comments and colour scale can be set with V A four options are available comments and colour scale default colour scale only annotations only or none The colour scale can be displayed in a secondary window with V C Please note that later changes on the scale won t be reflected on this display The annotations can also be positioned to the left and right of the picture or at the bottom and top which toggled with V O for orientation of annotations this setting will also be reflected on the colour scale displayed in secondary windows The thickness
11. background colour from black to white V 1 Enhanced 1D display V K Display the temperature at the bottom V X Close secondary windows Display D L Display length scale D M Set length scale to be displayed D F Flip length scale horizontal to vertical D Z Zoom in D Y Zoom out D X Revert to previous zoom settings D 3 Three folded symmetry D 4 Four folded symmetry D 9 Nine folded symmetry D C Switch between mirror and translation symmetry D G Display grid D H Set number of grid lines D T RGB triangle display D I Miller Indices display D D Display the difference of two results D N Logarithmic scale D A Display absolute value of results Display B 2 Vector field display B 3 3D vector field display B S Modify settings for vector field display B X Display vector scale B B Modify colour of vectors Isolines I D Display isolines 1 1 9 Add 1 9 automatic isolines N Add arbitrary number of automatic isolines I A Add user defined isolines HR Remove an isoline IS Remove all isolines I V Print the values of the current isolines I B Bi coloured isolines kW Write a list of the coordinates of contour points 1 X Same as above for all time steps 3D 3 X Cutting plane type perpendicular to X axis 3 Y Cutting plane type perpendicular to Y axis 3 Z Cutting plane type perpendicular to Z axis 3 U Move cutting plane up 3 D Move cutting plane down 3 S Explicitly set cutting plane
12. d example N means press key N either lower or upper case The combination of keys D and E pressing key D then key E will be represented by D E For an improved readability the corresponding operation will be printed in underlined italics Known issues When using the graphical user interface not exiting nicely i e with the EX T button can lead to complications please avoid it Display_MICRESS Page 3 of 10 Time step operations These include going to the next N previous P last L or first F time steps Hopefully these operations should be self explanatory When several files are displayed simultaneously these operations can also be applied to a selection of the results only with respectively M N M P M L or M F Scale By default minimum and maximum are chosen as the extrema of the whole result file which implies that the entire file has to be read which might take some time for very large simulations unless the f option was set from the command line and then the automatic min and max are set from the local min and max of the first time step The available options are user defined min and max SM a secondary window is opened to let the user modify the min and max settings user defined range S R similar to the previous but min and max are set as median value and range use local min and max S D which sets the extrema from what is displayed which can be only part of the result for the curr
13. ent time step if the zoom is in use and finally revert to automatic i e global min and max S G if the f option was used the file is then read for the global extrema S F explicitly force the file to be re read to find out the global extrema Note if several result files are displayed the user will be prompted to select the solutions to which these operations should be applied to User defined settings will affect all solutions which are selected simultaneously Colour scale Various colour scales are available in Display MICRESS the default one being the standard Viso heat scale but a few others are also available They can be selected with C 1 11 for example C41 sets the default Viso heat scale and C 2 a black and white one C L loops through the available colour scales To select double digit colour scale without graphical user interface press 0 C 0 1 0 will select the tenth colour scale The tenth and eleventh colour scales respectively called with C 9 and C 010 are adaptive in the sense that they have ranges of colors and or transition points whose position in the scale can be reset by the user according the isoline values The brightness and contrast can be fiddled with by pressing C F or reset with C R This fiddling feature is performed by resetting the brightness with the normalised x coordinate of the mouse cursor on the active image and the brightness with y coordinate s If a GUI d
14. ese two points have been set the zoom box is drawn and can be refused by pressing the right mouse button or X in which case another zoom box can be set or accepted by pressing any other key Zoom out with D Y no progressive zooming out is done i e zoom options are directly reset to their default values i e full picture It is also possible to zoom back with D X please note that only one set of zoom settings is saved If the simulation set up takes advantage on known symmetries or periodicities of the system and restricts the domain to part of the real space area it is sometimes handy to display respectively three four or nine times the simulation domain with respectively D 3 D 4 D 9 By default the copies of domain are mirrored but they can also be tranlsated which can be toggled on and off with D C To allow readier positioning a grid can be displayed with D G The default number of subdivisions is 5 but this can be adjusted with D H Two additional display modes are available RGB triangle and Miller Indices respectively with D T and D both are based on operations on the colour table and can only be used for all the displayed results The RGB triangle mode available with three solutions only plots a composite of them where the colour of a cell is the corresponding intensity of red green and blue calculated from the displayed minimum and maximum The Miller indices output of MICRESS can
15. evice is used the user has to click to set the cursor s position after calling this feature The colour scale can also be inverted with C l The minimum and maximum of the colour scale can be cut off i e respectively replaced with black and white with C C The current colour scale can also be reset in a stepwise fashion with C S It is possible to specify the number of step with CU user defined and to toggle on and off the use of this input with C T To break some unfortunate patterns when displaying grain output it can be interesting to use a stepwise colour scale and randomise it with C K These previous features are unfortunately not available under Windows due to a communication problem between PGPlot and GrWin Animation Display MICRESS supports animation A R will display one time step and then automatically switch to the next looping over the whole file Unfortunately it is not possible to interrupt the animation short of killing the program A E starts an animation to the last output The animation settings display time for each time step and number of loops can be changed with A S The display time might actually have to be extended to let the program proceed to the next time step in the case of large result files or simultaneous display of several solutions Display_MICRESS Page 4 of 10 View This category regroups various operations related to the graphical window settings Reset number of panels
16. from the main interface under Transfer MICRESS Remove Outputs Help Key H displays the summary of available options Exit To exit Display MICRESS press the right mouse button or X Final remarks As previously mentioned the graphical features of Display MICRESS are performed by the PGPlot library www astro caltech edu tjp pgplot The image output in PNG format Portable Network Graphics is made possible by the PNG library www libpng org and Z library www zlib net The Z library also handles compression and decompression of files by calling its minimal implementation MiniGZip The screen driver under Windows is from GrWin http sodg1 sci shizuoka ac jp grwinlib english Please visit their home pages The first implementation of Display MICRESS was strongly inspired by the PGPlot demo 4 Display MICRESS is not a commercial product it is provided as is on a courtesy basis Though Display MICRESS is convenient and pleasant to use it was unfortunately not actually meant to be a toy therefore some apparent limitations result from a use that was simply not considered to be of interest to the post processing of MICRESS results or even not intended altogether Summary of the shortcuts Group Shortcut Description Time step N Display the next output P Go back to the previous output L Go to
17. he curve s for the current time step R D Images of the curve s for all time steps R S Image of the curves for all time steps R M Image of the curves for a selection of time steps R F Front Tracking text output R F Front Tracking curve output R P Scan point text output R Q Scan point position output R R Scan point curve output Data information W M Measure distance W C Print coordinates and field value s for a point W A Measure angle W H Measure angle with the horizontal W V Measure angle with the vertical W E Print average and extrema from the current display W D Compare two files for the current time step W F Compare two files for all time steps W P Pin point cell pointer We Print information about MICRESS version W G Print information about the geometry Remove output K Remove current time step from output file s Help H Display the summary of available options Exit X Exit Display_MICRESS Page 10 of 10
18. lected simultaneously 3D Display MICRESS can display 2D cuts perpendicular to the main axis of 3D simulations The cutting plane type i e perpendicular to X axis Y axis or Z axis can be set respectively with 3 X 3 Y or 3 Z It is also possible to change the cutting plane position by moving it up increasing intercept coordinate or down with 3 U and 3 D or setting the value with 3 S Outputs Display MICRESS supports image various formats and ASCII outputs All these are done with current display settings scale colour representation zoom parameters etc and can be done for current time step or batch processed meaning that they will be performed for all time steps Image output of current time step O I of all time steps O J O L and O H respectively request writing out of larger or high resolution images ASCII output can be written out with O A and O B respectively without and with batch processing All the batch outputs have by default a name based on the time stamp from the current MICRESS output this can toggled on and off to numbering with O N An image of the colour scale only can be generated with O C Please note that the orientation of this image depends on the orientation of the annotations The default image driver is transparent background PNG Portable Networks Graphic which can be selected with the keys O T but can also be switched to opaque background PNG with O 0 or G
19. n ASCII gt r rename set of results from UNIX s naming to gt z compress output file Windows or vice versa Default plain file in binary not compressed gt output file in ASCII not compressed User interface typographical conventions Display MICRESS has a full fledged graphical front end DP_MICRESS which also acts as a wrapper to Display_MICRESS itself The following describes the use with keyboard shortcuts via the graphical front end or not All operations can be called by hot keys which are not case dependent e g key f and key F are considered to be identical Keyboard input Apart from the alphanumeric characters the following keys are also available Escape erases the current input and Tab validate the current input and go the next if any UNIX and Linux environment The DP MICRESS interfaces can be called with g flag it is possible to call it with only this flag then an interface to create the command line is displayed or with a complete command line in which case only the run time interface is called MS Windows Double clicking a MICRESS result file will start Display_MICRESS with the default settings otherwise a geoF file should be double clicked to display various files at the same time or call Transfer_MICRESS for example Please see Installing Display MICRESS under Windows Typographical conventions Keys to be pressed will be printed in italics bol
20. orresponding scan position output are of course identical to the ones from Virtual EDX Similarly for Scan Point text outputs RP position output R Q and curve output RR are available Data information The distance between two selected points can be displayed with W M measure distance Similarly the coordinates of a given point along with the corresponding field values can be printed with W C coordinates Arbitrary angles can be measured with W A angles with respectively with the horizontal or the vertical can be measured with W H and W V The average minimum and maximum from the current display are also available with W E extrema To compare diff two results press W D the user is then prompted for a threshold value significant difference allowing some numerical noise to be ignored The same can also be applied sequentially to all outouts with W F A MICRESS cell pointer can be pin pointed with W P Information about the time when the last output was written and the MICRESS and Display MICRESS versions can be printed out with W Information about the geometry can be printed out with W G Display_MICRESS Page 7 of 10 Remove output The current output can be removed from the displayed files with key K Please note that there is no undo for this feature the output is permanently removed from the file s Please note that a graphical interface to this feature is also available
21. which also disable it Also applies to all subsequent Virtual EDX outputs Once a line has been set it is possible to scan it for a given value over all the time steps this feature provides a convenient way of tracking a front and can be called with E F lt gives the distance from the beginning of the scan line first point selected of the first occurrence of the set value if this value is not found 1 will be reported It is also possible to display the evolution over time of the value of the field variable for a given point with the Scan Point feature which works in a very similar way to the Virtual EDX it can be called with E P Note if several result files are displayed the user will be prompted to select which solution s should be scanned This applies in a similar way to the Virtual EDX outputs Virtual EDX outputs Text output for current time step creates an ASCII file with the results of the scan R T it is also available for all time steps RU Scan position output writes an image with the position of the scan line similarly for current time step Rel or for all time steps RJ An image of the curves is also available respectively with R C forthe current time step and R D for all time steps lt is also possible to generate a single plot with the scans for all time steps with R S or a selection of them with R M For Front Tracking text output RF and curve output RG are available the c
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