nnm:visualization
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nnm:visualization [2019/03/07 12:33] stefan.birner [Overlay feature] |
nnm:visualization [2020/10/23 09:43] nextnanowikiadmin removed |
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| - | ====== Output format ====== | + | ====== Tab: Output ====== |
| + | |||
| + | ===== Output format ===== | ||
| nextnanomat can display the following output formats. | nextnanomat can display the following output formats. | ||
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| </code> | </code> | ||
| - | * ''.fld'' - 1D/2D/3D [[http://www.nextnano.com/nextnano3/input_parser/keywords/output-file-format.htm|AVS data format]] (rectilinear grid) - scalar field $f(x,y,z)$ or vector field $\mathbf{F}(x,y,z)$. | + | * ''.vtr'' - 2D/3D [[http://www.nextnano.com/nextnano3/input_parser/keywords/output-file-format.htm|VTK data format]] (rectilinear grid) - scalar field $f(x,y,z)$ or vector field $\mathbf{F}(x,y,z)$. ''.vtr'' files can be viewed using the [[nnm:visualization#d_visualizationparaview|Paraview]] software which is a full 3D visualization software while nextnanomat only displays 2D slices of 3D data files. |
| - | * ''.vtr'' - 2D/3D [[http://www.nextnano.com/nextnano3/input_parser/keywords/output-file-format.htm|VTK data format]] (rectilinear grid) - scalar field $f(x,y,z)$ or vector field $\mathbf{F}(x,y,z)$. | + | * ''.fld'' - 1D/2D/3D [[http://www.nextnano.com/nextnano3/input_parser/keywords/output-file-format.htm|AVS data format]] (rectilinear grid) - scalar field $f(x,y,z)$ or vector field $\mathbf{F}(x,y,z)$. |
| If a file extension is unknown it is treated as if it were a ''.txt'' file. | If a file extension is unknown it is treated as if it were a ''.txt'' file. | ||
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| ====== Overlay feature ====== | ====== Overlay feature ====== | ||
| - | For the best experience when visually analyzing the results of the simulation, it is sometimes necessary to look at different files at the same time. We call this the Overlay feature, it is very easy. | + | For the best experience when visually analyzing the results of the simulation, it is sometimes necessary to look at different files at the same time. We call this the Overlay feature. |
| {{:nnm:overlay.jpg?nolink&300 |}} | {{:nnm:overlay.jpg?nolink&300 |}} | ||
| Line 87: | Line 89: | ||
| The data of **2D/3D-plots** is directly stored within the *.plt file, so there is nothing to consider when moving these files. | The data of **2D/3D-plots** is directly stored within the *.plt file, so there is nothing to consider when moving these files. | ||
| - | (So why isn't this done alike for 1D-plots? Because with the overlay feature you have the possibility to export nearly unlimited *.dat files in only one *.plt file. If all this data would be duplicated and transferred into the *.plt file, it would simply become to big.) | + | (So why isn't this done alike for 1D-plots? Because with the overlay feature you have the possibility to export nearly unlimited *.dat files in only one *.plt file. If all this data would be duplicated and transferred into the *.plt file, it would simply get to big.) |
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| ===== Format options ===== | ===== Format options ===== | ||
| + | To edit gnuplot commands, open the <nowiki>"</nowiki>.plt<nowiki>"</nowiki> file with your text editor. | ||
| + | |||
| + | === Semi-log plot === | ||
| + | * ''set logscale x'' | ||
| + | * ''set logscale y'' | ||
| === Change the line thickness (''lw 4'') === | === Change the line thickness (''lw 4'') === | ||
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| * ''plot 'D:\density_hole.dat' using 1:2 title <nowiki>"</nowiki>p (10^18 cm^-3)<nowiki>"</nowiki> noenhanced <nowiki>...</nowiki>'' | * ''plot 'D:\density_hole.dat' using 1:2 title <nowiki>"</nowiki>p (10^18 cm^-3)<nowiki>"</nowiki> noenhanced <nowiki>...</nowiki>'' | ||
| - | === Change range $[x_{min},x_{max}]$ and $[y_{min},y_{max}]$ of graph === | + | === Change range $[x_{min},x_{max}]$ and $[y_{min},y_{max}]$ of the graph === |
| * ''set xrange [-0.3:100.3]'' | * ''set xrange [-0.3:100.3]'' | ||
| * ''set xrange [0:100]'' | * ''set xrange [0:100]'' | ||
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| * ''set yrange [-1.0:0.5]'' | * ''set yrange [-1.0:0.5]'' | ||
| - | === Remove grid === | + | === Set/Remove grid === |
| * ''set grid'' | * ''set grid'' | ||
| * ''unset grid'' | * ''unset grid'' | ||
| Line 122: | Line 129: | ||
| * ''set border lw 3'' | * ''set border lw 3'' | ||
| - | === Remove legend === | + | === Set/Remove legend === |
| * ''set key on <nowiki>...</nowiki>'' | * ''set key on <nowiki>...</nowiki>'' | ||
| * ''set key off <nowiki>...</nowiki>'' | * ''set key off <nowiki>...</nowiki>'' | ||
| - | === Remove box around legend ("box") === | + | === Set/Remove box around legend ("box") === |
| * ''set key on <nowiki>...</nowiki> box'' | * ''set key on <nowiki>...</nowiki> box'' | ||
| * ''set key on <nowiki>...</nowiki> nobox'' | * ''set key on <nowiki>...</nowiki> nobox'' | ||
| - | === Increase fonz size in legend === | + | === Increase font size in legend === |
| * ''set key on <nowiki>...</nowiki> font <nowiki>"</nowiki>sans - serif,14<nowiki>"</nowiki>'' | * ''set key on <nowiki>...</nowiki> font <nowiki>"</nowiki>sans - serif,14<nowiki>"</nowiki>'' | ||
| * ''set key on <nowiki>...</nowiki> font <nowiki>"</nowiki>sans - serif,18<nowiki>"</nowiki>'' | * ''set key on <nowiki>...</nowiki> font <nowiki>"</nowiki>sans - serif,18<nowiki>"</nowiki>'' | ||
| + | |||
| + | === Specify the location of legend === | ||
| + | * ''set key left top inside <nowiki>...</nowiki>'' | ||
| + | * ''set key right bottom outside <nowiki>...</nowiki>'' | ||
| === Remove line from legend ("notitle")=== | === Remove line from legend ("notitle")=== | ||
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| === Add Greek letter to line in legend ("{/Symbol G}" "enhanced")=== | === Add Greek letter to line in legend ("{/Symbol G}" "enhanced")=== | ||
| * ''using 1:2 title <nowiki>"</nowiki>{/Symbol G} [eV]<nowiki>"</nowiki> enhanced'' produces $\Gamma$ | * ''using 1:2 title <nowiki>"</nowiki>{/Symbol G} [eV]<nowiki>"</nowiki> enhanced'' produces $\Gamma$ | ||
| + | * e, l, m, q produce $\epsilon, \lambda, \mu, \theta$, respectively. | ||
| + | |||
| + | === Add a label to the point $(x,y)$ in the plot === | ||
| + | * ''set label <nowiki>"</nowiki>label<nowiki>"</nowiki> at 0.5,1.5'' | ||
| + | |||
| + | === Add an arrow === | ||
| + | * ''set arrow from 1.5,0.3 to 4,2'' | ||
| + | |||
| + | === Graph Title === | ||
| + | * ''set title <nowiki>"</nowiki>title<nowiki>"</nowiki> font <nowiki>"</nowiki>sans - serif,18<nowiki>"</nowiki>'' | ||
| === Generate high quality graphs === | === Generate high quality graphs === | ||
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| * Open the saved ''.svg'' file with Inkscape ([[https://inkscape.org|www.inkscape.org]]) | * Open the saved ''.svg'' file with Inkscape ([[https://inkscape.org|www.inkscape.org]]) | ||
| * ''File'' => ''Export .PNG Image...'' => Select ''Drawing'' => ''Export'' | * ''File'' => ''Export .PNG Image...'' => Select ''Drawing'' => ''Export'' | ||
| + | |||
| + | ====== 3D Visualization: Paraview ====== | ||
| + | - Install the free software [[https://www.paraview.org|Paraview]] on your computer | ||
| + | - Within nextnanomat: | ||
| + | - in 'Tools' >> 'Options' >> 'View', write the path of the Paraview executable in the user computer, e.g. ''C:\Program Files\ParaView 5.6.0-Windows-msvc2015-64bit\bin\paraview.exe'' | ||
| + | - Select a 3D ''.vtr'' file of the simulation output folder and click on the 'Export and open in specific format' button. Choose 'Open File with Paraview' ( Paraview will open automatically.) | ||
| + | - Withing Paraview: | ||
| + | - (The selected file should be automatically highlighted in Paraview.) Click on 'Apply'. | ||
| + | - Other settings: | ||
| + | - Representation: Surface | ||
| + | - Cell/Point Array Status: Choose the array to be displayed. For example, one can display the file ''bandedges.vtr'' and choose the array ''Gamma'' that corresponds to the \Gamma conduction band. Click on 'Apply'. | ||
| + | - Coloring: Choose the array to be displayed. (Gamma, in this example) | ||
| + | |||
| + | Now you can play with the tool rotating, changing opacity and adding filters. | ||
| + | Paraview is a very rich tool: It requires some time to explore all its capabilities. | ||
| + | We recommend investing some time to learn about its filters. First the file should be highlighted and then to click 'Filter' >> 'Alphabetical' | ||
| + | Some interesting ones are: | ||
| + | * Edit cells by region | ||
| + | * Calculator | ||
| + | * Contour | ||
| + | | ||
| + | Using 'File' >> 'Save State', the compute can store the value of all variables, to reproduce again the representation, if necessary (by loading the state). This is useful for generation of scripts. | ||
| + | |||
| + | Having more questions, we recommend a good tutorial from TACC, although there exist plenty of examples on the web: [[https://portal.tacc.utexas.edu/c/document_library/get_file?uuid=01dd202d-58c6-4b46-8310-b6d7087372ac&groupId=13601|https://portal.tacc.utexas.edu/c/document_library/get_file?uuid=01dd202d-58c6-4b46-8310-b6d7087372ac&groupId=13601]] | ||
| + | |||
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