Editing Generate figures

go back to [[Main Page]], [[Computational Resources]], [[Scripts]] or [[VASP]], [[Scripts for VASP]]

To map several molecules at once, put together the CONTCAR files (CONT*). Then use the attached scrip with xcrysden.

The script has three parts.

===1. Convert POSCAR/CONTCAR to *.xsf===

In order to use this tool, you will need the program v2xsf. Find attached here [[Image:Xcrysden.tgz]] or here [[https://nano.tu-dresden.de/~jkunstmann/software.html]]. First, put v2xsf in your /home/bin/ folder and make it executable (chmod +x v2xsf). Then, put all your CONTCAR/POSCAR in the same folder with the extension *.vasp and execute the following command in a terminal: 

 for j in `ls *.vasp` ; do v2xsf $j ; done

If you are working with surfaces, you may want to eliminate the bottom layer before that. This example is for (111) metals with 2sqrt(3)×2sqrt(3) symmetry. 

 for j in `ls *.vasp` ; do sed -i "7s/48/36/g" $j ; sed -i "10,21d" $j ; done

===2. Script preparation===
XCrysDen can work with a *.tcl script as input file. This utility will build that script for you:

 #!/bin/bash
 
 # # # # # # # # # # # # # # # # # # # # # # # # #
 # Created by Rodrigo García-Muelas            #
 #                                           #
 # Suitable for VASP 5.x                  #   
 # First review:  July 10, 2012.             #
 # Current review: Oct 16, 2018.              #
 # # # # # # # # # # # # # # # # # # # # # # # # # 
 #
 # Notes:
 # 1. The input files should be *.vasp
 # 2. Requires v2xsf conversor <--- Available on VASP webpage.
 # 3. Inspired by a similar creation from David Karhanek.
 # 4. Remember to write in the terminal: for j in `ls *.vasp` ; do v2xsf $j ; done
 #
 # remove old tcl scripts (this section needs to be fix)
 if [ -e epsprinting.tcl ] ; then echo "removing old epsprinting.tcl" ; rm -f epsprinting.tcl ; fi
 #
 # comprobates if you have *.xsf.gz files
 if [ -z `ls *.vasp.xsf.gz` ] ; then 
 echo "Please execute: "
 echo "for j in \`ls *.vasp\` ; do sed -i "7s/48/36/g" \$j ; sed -i "10,21d" \$j ; done"
 echo "for j in \`ls *.vasp\` ; do v2xsf \$j ; done" 
 echo "All your POSCAR's should have .vasp extension"
 exit
 fi 
 #
 # Note: you can use: "resize 640 480" or "resize 800 1000" or "resize 640 480", etc. Limit around 4000.
 
 #####################
 # Loop for side view:
 for i in `ls *.vasp.xsf.gz`
 do   
 cat >>epsprinting.tcl<<!
 scripting::open --xsf $i
 scripting::displayWindow resize 800 800
 xc_newvalue .mesa 8  0 1.000000 1.000000 1.000000
 xc_newvalue .mesa 8  1 1.000000 1.000000 1.000000
 xc_newvalue .mesa 8  3 1.000000 1.000000 0.500000
 xc_newvalue .mesa 8  5 0.670000 0.330000 0.000000
 xc_newvalue .mesa 8  6 0.250000 0.250000 0.250000
 xc_newvalue .mesa 8  7 0.000000 0.000000 1.000000
 xc_newvalue .mesa 8  8 1.000000 0.000000 0.000000
 xc_newvalue .mesa 8  9 0.000000 1.000000 0.000000
 xc_newvalue .mesa 8 16 0.906000 0.882000 0.275000
 xc_newvalue .mesa 8 26 1.000000 0.930000 0.870000 
 xc_newvalue .mesa 8 27 0.870000 0.930000 1.000000
 xc_newvalue .mesa 8 28 0.800000 1.000000 1.000000
 xc_newvalue .mesa 8 29 1.000000 0.920000 0.880000
 xc_newvalue .mesa 8 30 0.900000 0.900000 0.900000
 xc_newvalue .mesa 8 34 0.951000 0.882000 0.230000
 xc_newvalue .mesa 8 44 1.000000 0.800000 1.000000
 xc_newvalue .mesa 8 45 1.000000 0.800000 1.000000
 xc_newvalue .mesa 8 46 0.900000 0.900000 1.000000
 xc_newvalue .mesa 8 47 0.933333 0.933333 0.933333
 xc_newvalue .mesa 8 48 1.000000 0.880000 0.920000
 xc_newvalue .mesa 8 49 0.925000 0.925000 1.000000
 xc_newvalue .mesa 8 52 0.996000 0.882000 0.185000
 xc_newvalue .mesa 8 75 1.000000 0.950000 0.850000
 xc_newvalue .mesa 8 76 1.000000 0.900000 0.900000
 xc_newvalue .mesa 8 77 1.000000 0.800000 1.000000
 xc_newvalue .mesa 8 78 0.900000 1.000000 0.900000
 xc_newvalue .mesa 8 79 1.000000 1.000000 0.800000
 xc_newvalue .mesa 4  1 0.90000
 xc_newvalue .mesa 4  3 0.90000
 xc_newvalue .mesa 4  5 1.50000
 xc_newvalue .mesa 4  6 2.05000
 xc_newvalue .mesa 4  7 1.90000
 xc_newvalue .mesa 4  8 1.80000
 xc_newvalue .mesa 4  9 1.70000
 xc_newvalue .mesa 4 16 2.90000
 xc_newvalue .mesa 4 26 3.10000
 xc_newvalue .mesa 4 27 3.05000
 xc_newvalue .mesa 4 28 2.95000
 xc_newvalue .mesa 4 29 2.95000
 xc_newvalue .mesa 4 30 2.95000
 xc_newvalue .mesa 4 34 3.05000
 xc_newvalue .mesa 4 44 3.55000
 xc_newvalue .mesa 4 45 3.47000
 xc_newvalue .mesa 4 46 3.40000
 xc_newvalue .mesa 4 47 3.45000
 xc_newvalue .mesa 4 48 3.50000
 xc_newvalue .mesa 4 49 2.40000
 xc_newvalue .mesa 4 52 3.20000
 xc_newvalue .mesa 4 75 3.55000
 xc_newvalue .mesa 4 76 3.55000
 xc_newvalue .mesa 4 77 3.55000
 xc_newvalue .mesa 4 78 3.55000
 xc_newvalue .mesa 4 79 3.55000
 scripting::displayMode3D BallStick
 set myParam(TESSELLATION)      99.00
 set myParam(COV_SCALE)          1.25
 set myParam(FRAMECOL)         { 0.00 0.00 0.00 } 
 set myParam(BACKGROUND)       { 1.00 1.00 1.00 }
 scripting::load_myParam
 scripting::display off crystal-cells 
 scripting::displayMode3D BallStick
 scripting::display as cell-unit symm
 scripting::buildCrystal 1 1 1
 xc_translparam set 0 0 1 
 scripting::rotate x 90
 scripting::zoom 2
 scripting::printToFile ${i%\.vasp.xsf.gz}_s.png
 
 !
 done
 
 # Loop for top view:
 for i in `ls *.vasp.xsf.gz`
 do                              # resize 640 480
 cat >>epsprinting.tcl<<!
 scripting::open --xsf $i
 scripting::displayWindow resize 800 800
 xc_newvalue .mesa 8  0 1.000000 1.000000 1.000000
 xc_newvalue .mesa 8  1 1.000000 1.000000 1.000000
 xc_newvalue .mesa 8  3 1.000000 1.000000 0.500000
 xc_newvalue .mesa 8  5 0.670000 0.330000 0.000000
 xc_newvalue .mesa 8  6 0.250000 0.250000 0.250000
 xc_newvalue .mesa 8  7 0.000000 0.000000 1.000000
 xc_newvalue .mesa 8  8 1.000000 0.000000 0.000000
 xc_newvalue .mesa 8  9 0.000000 1.000000 0.000000
 xc_newvalue .mesa 8 16 0.906000 0.882000 0.275000
 xc_newvalue .mesa 8 26 1.000000 0.930000 0.870000 
 xc_newvalue .mesa 8 27 0.870000 0.930000 1.000000
 xc_newvalue .mesa 8 28 0.800000 1.000000 1.000000
 xc_newvalue .mesa 8 29 1.000000 0.920000 0.880000
 xc_newvalue .mesa 8 30 0.900000 0.900000 0.900000
 xc_newvalue .mesa 8 34 0.951000 0.882000 0.230000
 xc_newvalue .mesa 8 44 1.000000 0.800000 1.000000
 xc_newvalue .mesa 8 45 1.000000 0.800000 1.000000
 xc_newvalue .mesa 8 46 0.900000 0.900000 1.000000
 xc_newvalue .mesa 8 47 0.933333 0.933333 0.933333
 xc_newvalue .mesa 8 48 1.000000 0.880000 0.920000
 xc_newvalue .mesa 8 49 0.925000 0.925000 1.000000
 xc_newvalue .mesa 8 52 0.996000 0.882000 0.185000
 xc_newvalue .mesa 8 75 1.000000 0.950000 0.850000
 xc_newvalue .mesa 8 76 1.000000 0.900000 0.900000
 xc_newvalue .mesa 8 77 1.000000 0.800000 1.000000
 xc_newvalue .mesa 8 78 0.900000 1.000000 0.900000
 xc_newvalue .mesa 8 79 1.000000 1.000000 0.800000
 xc_newvalue .mesa 4  1 0.90000
 xc_newvalue .mesa 4  3 0.90000
 xc_newvalue .mesa 4  5 1.50000
 xc_newvalue .mesa 4  6 2.05000
 xc_newvalue .mesa 4  7 1.90000
 xc_newvalue .mesa 4  8 1.80000
 xc_newvalue .mesa 4  9 1.70000
 xc_newvalue .mesa 4 16 2.90000
 xc_newvalue .mesa 4 26 3.10000
 xc_newvalue .mesa 4 27 3.05000
 xc_newvalue .mesa 4 28 2.95000
 xc_newvalue .mesa 4 29 2.95000
 xc_newvalue .mesa 4 30 2.95000
 xc_newvalue .mesa 4 34 3.05000
 xc_newvalue .mesa 4 44 3.55000
 xc_newvalue .mesa 4 45 3.47000
 xc_newvalue .mesa 4 46 3.40000
 xc_newvalue .mesa 4 47 3.45000
 xc_newvalue .mesa 4 48 3.50000
 xc_newvalue .mesa 4 49 2.40000
 xc_newvalue .mesa 4 52 3.20000
 xc_newvalue .mesa 4 75 3.55000
 xc_newvalue .mesa 4 76 3.55000
 xc_newvalue .mesa 4 77 3.55000
 xc_newvalue .mesa 4 78 3.55000
 xc_newvalue .mesa 4 79 3.55000
 scripting::displayMode3D BallStick
 set myParam(TESSELLATION)      99.00
 set myParam(COV_SCALE)          1.25
 set myParam(FRAMECOL)         { 0.00 0.00 0.00 } 
 set myParam(BACKGROUND)       { 1.00 1.00 1.00 }
 scripting::load_myParam
 scripting::display on crystal-cells 
 scripting::displayMode3D BallStick
 scripting::display as cell-unit symm
 scripting::buildCrystal 1 1 1
 xc_translparam set 0 0 1 
 scripting::zoom 2
 scripting::printToFile ${i%\.vasp.xsf.gz}_t.png 
 
 !
 done
 
 echo "Now run XCrySDen in script mode: xcrysden -s epsprinting.tcl"


Explanation:

You can set the size of the window with the command below. Notice that a bigger window size imply a larger and heavier image.
 scripting::displayWindow resize 800 1000

You can change the colors of your atoms. The example shows H, C, O and Pt (Z=1,6,8,78) and colors white (1.00 1.00 1.00 RGB), gray, red and light green:
 xc_newvalue .mesa 8  1 1.000000 1.000000 1.000000
 xc_newvalue .mesa 8  6 0.250000 0.250000 0.250000
 xc_newvalue .mesa 8  8 1.000000 0.000000 0.000000
 xc_newvalue .mesa 8 78 0.800000 1.000000 0.800000

To change the size of the ball for each element, you have this part:
 xc_newvalue .mesa 4  1 0.90000
 xc_newvalue .mesa 4  6 2.05000
 xc_newvalue .mesa 4  8 1.80000
 xc_newvalue .mesa 4 78 3.55000

The quality of the texture can be adjusted with the tessellation factor. Use low values (20) for fast screening, tests, and images of internal use. Use large values (99) for publication-quality images.
 set myParam(TESSELLATION)      20.00

To colour the borders of the supercell in black:
 set myParam(FRAMECOL)          { 0.00 0.00 0.00 }

Set the background color as white to be printer-friendly.
 set myParam(BACKGROUND)        { 1.00 1.00 1.00 }

Build a 1×1×1 supercell
 scripting::buildCrystal 1 1 1 


Play with these parameters in order to focus your cell at your wish:
 scripting::rotate x 90
 scripting::zoom 2

Do NOT put comments in the epsprinting.tcl file.

===3. Printing and post-processing===

Run XCrysDen in scripting mode by typing:
 $ xcrysden -s epsprinting.tcl

Tips: 
* If you want to convert the background of an image from white to transparent, write in the command line: 

 convert -transparent white <input_file> <output_file>

* If you want to crop transparent spaces, write in the command line:
 convert -trim <input_file> <output_file>

* If you want to crop the side view images, do:
 convert -gravity Center -crop 120x30%+0+100\! <input_file> <output_file>

* You can also do ("x" and "y" directions, + for right/up , - for left/down:
 convert -crop +0-275 <input_file> <output_file>

* In batch mode:
 for j in *.png ; do echo $j ; convert -transparent white $j $j ; done
 for j in *.png ; do echo $j ; convert -trim $j $j ; done
 for j in *.png ; do echo $j ; convert -gravity Center -crop 120x30%+0+100\! $j $j ; done

* It would also work: 
 for j in `ls *.png` ; do echo $j ; convert -transparent white $j $j ; done
 for j in `ls *.png` ; do echo $j ; convert -trim $j $j ; done
 for j in `ls *.png` ; do echo $j ; convert -gravity Center -crop 120x30%+0+100\! $j $j ; done

* If you generated your figures in other formats (i.e. *.eps), and you want to convert them into png:
  for j in *eps ; do echo $j ; convert $j ${j%%.eps}.png ; done
  for j in *eps ; do echo $j ; convert -density 600 $j ${j%%.eps}.png ; done

* To remove the weird blue fog, as soon as it starts generating the images, press shift+x (Or menu: Modify > materials/fog/antialias parameters) and in "Emision colour" set the blue component to zero. Then "Update" and "Close". You may need to repeat the commands for the first images just to have it well done. 

For aditional commands, see [[http://www.xcrysden.org/doc/prog/contours.tcl.html]]

==Merging everything as a LaTeX table==
This script exemplifies how to prepare the input tex file for a series of NEB. It results in the table-temp.tex file:
 #!/bin/bash 
 # Rodrigo García-Muelas
 # Version 5 May 2021 
 
 outputf="table-temp.tex"    # output file  
 pathfig="./raw/"              # all figures are placed in a subfolder called raw, for have some order  
 
 rm -f $outputf
 
 #side view must be reduced by a factor x0.9315184 if there is a metal at (,0,0)
 qt="\includegraphics[width=0.2060\\textwidth]{$pathfig"
 qs="\includegraphics[width=0.2000\\textwidth,trim=0mm 105mm 0mm 120mm,clip=true]{$pathfig"
 
 touch $outputf 
 
 for k in `cat '0-list.txt'` ; do
 
 echo $k
 i=$k
 
 echo "\hline                                       "  >> $outputf
 echo "\multicolumn{4}{c}{ " $i " } \\\\*           "  >> $outputf
 
 echo $qt$i"-00_t.png} & " $qt$i"-02_t.png} & " $qt$i"-03_t.png} & " $qt$i"-05_t.png} \\\\* " >> $outputf
 echo $qs$i"-00_s.png} & " $qs$i"-02_s.png} & " $qs$i"-03_s.png} & " $qs$i"-05_s.png} \\\\  " >> $outputf
 
 done 


Then open this LaTeX file and compile it. It will call the previous table and compile all figures. 
 \documentclass[a4paper,10pt]{article}
 \usepackage[a4paper,portrait,bindingoffset=5mm,left=10mm,right=10mm,top=10mm,bottom=10mm,footskip=5mm]{geometry}
 \usepackage[utf8]{inputenc}
 \usepackage{graphicx}
 \usepackage{longtable}
 \graphicspath { {raw/} }
 
 % Title Page
 \title{Figures}
 \author{Rodrigo Garcia-Muelas}
 
 \begin{document}
 \maketitle
 
 %\begin{abstract}
 %\end{abstract}
 
 This is a NEB table automatically generated in LaTeX. 
 Perhaps you want to ``trim'' all figures before compiling with imagemagick.
 
 \begin{longtable}{ l l l l }
 \caption{Images 00, 02, 03, and 05 of a NEB }
 \label{t.figpca}  \\
 
   \hline
   00 & 02 & 03 & 05 \\
   \hline
   \endfirsthead
 
   \multicolumn{4}{c}{{\bfseries \tablename\ \thetable{} -- continued from previous page}} \\
   \hline
   00 & 02 & 03 & 05 \\ \hline
   \endhead
 
   \hline
   \multicolumn{4}{r}{{Continues on next page {} }} \\
   \endfoot
 
   \hline
   \endlastfoot
 
 \input{./table-temp}
 
 \end{longtable}
 
 \end{document} 

--[[User:Rgarcia|Rgarcia]] 19:23, 12 December 2012 (CET)