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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 File:Xcrysden.tgz or here [[1]]. 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

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.             #
# Second review: April 30, 2013.              #
# # # # # # # # # # # # # # # # # # # # # # # # # 
#
# 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 rm epsprinting.tcl ; fi
#
# comprobates if you have *.xsf.gz files
#if [ -e *.xsf.gz ] ; then
echo "Preparing TCL script for EPS export..."
#else
#echo 
#echo "Please execute:  for j in \`ls *.vasp\` ; do v2xsf \$j ; done" 
#echo "bye"
#echo 
#exit
#fi

for i in `ls *.xsf.gz`
do                              # resize 640 480
 cat >>epsprinting.tcl<<!
scripting::open --xsf $i
scripting::displayWindow resize 3200 4000
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 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 0.500000 0.300000
xc_newvalue .mesa 8 44 1.000000 0.900000 0.900000
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 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 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 44 3.55000
xc_newvalue .mesa 4 45 3.47000
xc_newvalue .mesa 4 46 3.40000
xc_newvalue .mesa 4 47 3.40000
xc_newvalue .mesa 4 78 3.55000
xc_newvalue .mesa 4 79 3.55000
scripting::displayMode3D BallStick
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 asymm
scripting::buildCrystal 1 1 1
xc_translparam set 0 0 1 
scripting::rotate x 90
scripting::zoom 2
scripting::printToFile ${i%\.vasp.xsf.gz}.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

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

• It would also work:

for j in `ls *.png` ; do convert -transparent white $j $j ; done
for j in `ls *.png` ; do convert -trim $j $j ; done
for j in `ls *.png` ; do 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 convert $j ${j%%.eps}.png ; done
 for j in *eps ; do convert -density 600 $j.eps ${j%%.eps}.png ; done

For aditional commands, see [[2]]

--Rgarcia 19:23, 12 December 2012 (CET)