Gowtham » Seventh Sense » BASH – vasp2xyz, A Script To Extract Coordinates From VASP

Seventh Sense Rambling about life's little things, in 7 ≡ 1 (mod 6) fashion

« BASH – Wrappers For qstat In NPACI ROCKS 5.2.2 | 2009 – The Year That Was »

BASH – vasp2xyz, A Script To Extract Coordinates From VASP

December 22nd, 2009 @ 17:00:54 | AWK, BASH, VASP

Users of VASP are often familiar with the struggles/hardships to easily visualize the coordinates from the output file [OUTCAR]. To that effect, I wrote the following script [with help at a crucial stage from Pat Krogel, CEC @ MTU]. It expects OUTCAR & POSCAR from a calculation to be in the same folder and when successfully completed, it results in OUTPUT_FILENAME.xyz – containing frame-by-frame [corresponding to each (optimization) step] XYZ co-ordinates of the system.

#! /bin/bash
 
# Script to extract the atomic positions (xyz) from 
# POSCAR & OUTCAR files of VASP and write them to a 
# file, to be used with Jmol, MolDen and such other
# third party programs
 
# First written: Gowtham, Tue, 22 Dec 2009 11:11:12 -0500
# Last modified: Gowtham, Tue, 22 Dec 2009 16:29:36 -0500
 
# Essential VASP Files
# If missing, quit the program
export POSCAR="POSCAR"
export OUTCAR="OUTCAR"
 
if [[ -e $POSCAR || -e $OUTCAR ]];
then
  echo
  echo "  $POSCAR & $OUTCAR found"
else
  echo
  echo "  ERROR : POSCAR &/or OUTCAR missing"
  echo
  exit
fi
 
# Output Filename 
# If missing, quit the program
export OUTPUT=$1
 
if [ $# != 1 ];
then
  echo
  echo "  ERROR : OUTPUT_FILENAME Missing"
  echo "  Usage : vasp2xyz.sh OUTPUT_FILENAME"
  echo
  exit
fi
 
# Delete scratch files
rm -f Final.tmp.*
rm -f $OUTPUT.xyz
 
# Atoms related information
# Extracted from POSCAR & OUTCAR
 
# Total number of atom types
# Pat Krogel: Tue, 22 Dec 2009 13:13:48 -050
declare -a ATOM_TYPE=(`sed -n '6 p' $POSCAR`)
export ATOM_TYPE_TOTAL=${#ATOM_TYPE[@]}
 
# Total number of atoms
export ATOMS_TOTAL=0
export i=0
while [[ "$i" -lt "$ATOM_TYPE_TOTAL" ]];
do
  export iATOM_TYPE=${ATOM_TYPE[$i]}
  export ATOMS_TOTAL=`expr $ATOMS_TOTAL + $iATOM_TYPE`
  export i=`expr $i + 1`
done
 
# Atom labels
declare -a ATOM_LABEL=(`grep "POTCAR:" $OUTCAR | head -$ATOM_TYPE_TOTAL | awk '{print $3}' | sed -e 's/_.*//g'`)
export ATOM_LABEL_TOTAL=${#ATOM_LABEL[@]}
 
# Print2Screen
if [[ "$ATOM_TYPE_TOTAL" != "$ATOM_LABEL_TOTAL" ]];
then
  echo
  echo "  ERROR : Atom Type Total ($ATOM_TYPE_TOTAL) does NOT"
  echo "          match Atom Label Count ($ATOM_LABEL_COUNT)"
  echo "  Please make sure OUTCAR & POSCAR are from the same"
  echo "  system and calculation"
  echo 
  exit
else
  echo
  echo "  Number of Atom Types   :" $ATOM_TYPE_TOTAL
  echo "  Atom Type              :" ${ATOM_LABEL[@]}
  echo "  Atom Type Count        :" ${ATOM_TYPE[@]}
  echo "  Total Number of Atoms  :" $ATOMS_TOTAL
 
  # ATOM_LABEL_2 is an array of atom labels
  # with each atom label appearing an appropriate
  # number of times, to a total of $ATOMS_TOTAL
  declare -a ATOM_LABEL_2
  export REPEAT=0
  export j=0
 
  while [[ "$j" -lt "$ATOM_TYPE_TOTAL" ]]; 
  do
    export k=1
 
    while [[ "$k" -le "${ATOM_TYPE[$j]}" ]]; 
    do
      export REPEAT=`expr $REPEAT + 1`
      export k=`expr $k + 1`
      ATOM_LABEL_2[$REPEAT]=${ATOM_LABEL[$j]}
    done
 
    export j=`expr $j + 1`
  done
# echo ${ATOM_LABEL_2[@]}
# echo ${#ATOM_LABEL_2[@]}
 
  # Record the line numbers where coordinates are written
  # in OUTCAR. Actual coordinates begin 2 lines below
  # the recorded numbers
  grep -n "POSITION" $OUTCAR | sed -e 's/:/ /g' | sed -e 's/POSITION.*//g' > LINE_NUMBERS.tmp
 
  export FRAME_NUMBER=1
  while read START
  do
    export START_HERE=`expr $START + 2`
    export END_HERE=`expr $START_HERE + $ATOMS_TOTAL - 1`
 
    echo "$ATOMS_TOTAL" >> $OUTPUT.xyz
    echo "# Frame Number: $FRAME_NUMBER" >> $OUTPUT.xyz
    sed -n "$START_HERE,$END_HERE p" $OUTCAR | awk '{printf "%12.8f %12.8f %12.8f\n", $1, $2, $3}' > Final.tmp.$FRAME_NUMBER
 
    export l=1
    while read X Y Z
    do
      echo ${ATOM_LABEL_2[$l]} $X $Y $Z > Final.tmp.$FRAME_NUMBER.$l
      awk '{ printf "%-3s %12.8f %12.8f %12.8f\n", $1, $2, $3, $4 }' Final.tmp.$FRAME_NUMBER.$l >> $OUTPUT.xyz
      export l=`expr $l + 1`
    done<Final.tmp.$FRAME_NUMBER
 
    export FRAME_NUMBER=`expr $FRAME_NUMBER + 1`
  done<LINE_NUMBERS.tmp
 
  export FRAMES_TOTAL=`expr $FRAME_NUMBER - 1`
  echo "  Total Number of Frames :" $FRAMES_TOTAL
  echo
fi
 
# Delete scratch files
rm -f LINE_NUMBERS.tmp 
rm -f Final.tmp.*

Test Case

If POSCAR and OUTCAR aren’t handily available for testing, one could download the following:

POSCAR | OUTCAR

vasp2xyz

Running vasp2xyz.sh

vasp2xyz

Resulting xyz file

vasp2xyz

xyz file visualized with Jmol

If you have suggestions to make this better/efficient, please do post them as comments.

Responses to BASH – vasp2xyz, A Script To Extract Coordinates From VASP

computer ram says:

2009.12.27 at 22:15:25

Hi…
That is such a nice information. It can be very helpful to a lot of people here. Thank you so much for sharing.

Reply
Fendy says:

2010.01.22 at 00:52:06

Hi….I already save the script with the name vasp2xyz.sh but I have some problem to execute the program….This is what happen when I want to use the program :

[revival@localhost Program]$ vasp2xyz
bash: vasp2xyz: command not found

Could someone give me an answer about this???

GBU

Reply
Fendy says:

2010.01.22 at 00:53:31

I also try like this but no result :

[revival@localhost Program]$ vasp2xyz.sh ONCH
bash: vasp2xyz.sh: command not found

Any comment???

GBU

Reply
- Gowtham says:
  
  2010.01.22 at 08:12:15
  
  It is important [and often assumed] that you place these programs/scripts in one of the locations defined by PATH variable. You could check for this by running the command:
  
  echo $PATH
  
  One such common location for keeping user’s personal collection of scripts is ‘bin‘ folder within your $HOME directory. Be sure to change the permission of the downloaded script to 755 [or at least 700] by running the command:
  
  chmod 700 vasp2xyz.sh
  
  Assuming that you are using the default shell [/bin/bash] for your login, you will need to add the following line to $HOME/.bashrc file:
  
  export PATH="$HOME/bin:$PATH"
  
  Save the file and run the command:
  
  . $HOME/.bashrc
  
  Once these [customary] steps are completed, you can call vasp2xyz.sh [or any such script stored in your 'bin' folder] from just about any other folder.
  
  Hope this helps.
  
  Reply
  - Fendy says:
    
    2010.01.22 at 21:02:07
    
    Dear Gowtham,,,,thanks so much for your reply and I did like you told me,,,and this is the result :
    
    I change the mode of vasp2xyz
    [revival@localhost Program]$ chmod 700 vasp2xyz.sh
    
    I put the bin path into the .bashrc
    [revival@localhost Program]$ vi ~/.bashrc
    
    #——————————-
    #this is for vasp2xyz.sh
    
    export PATH=”$HOME/bin:$PATH”
    
    and then I try again to execute the vasp2xyz.sh and it doesn’t work
    
    [revival@localhost Program]$ vasp2xyz.sh
    bash: vasp2xyz.sh: command not found
    
    This is the $PATH
    
    [revival@localhost Program]$ echo $PATH
    /home/revival/bin:/home/revival/vtstscripts:/home/revival/ase/tools:/home/revival/XCrySDen-1.4.1bin-shared:/home/revival/vtstscripts:/home/revival/ase/tools:/home/revival/XCrySDen-1.4.1bin-shared:/usr/bin:/bin:/usr/local/bin:/usr/X11R6/bin/:/usr/games:/usr/lib/qt4/bin:/home/revival/XCrySDen-1.4.1bin-shared/scripts:/home/revival/XCrySDen-1.4.1bin-shared/util:/home/revival/bin:/home/revival/XCrySDen-1.4.1bin-shared/scripts:/home/revival/XCrySDen-1.4.1bin-shared/util
    
    Is there anything that I miss to do???? I’m sorry to ask a very basic question like this because I’m still a newbee in linux,,,,this is the first year for me to learn linux but I’m improving much after I read your reply
    
    Thanks so much Gowtham
    
    GBU
    
    Reply
    - Gowtham says:
      
      2010.01.22 at 21:09:06
      
      I am kind of stumped. Is there any output if you type
      
      $HOME/bin/vasp2xyz.sh ??
      
      Reply
      - Fendy says:
        
        2010.01.22 at 21:17:51
        
        Dear Gowtham
        
        This is the result
        
        [revival@localhost bin]$ $HOME/bin/vasp2xyz.sh
        bash: /home/revival/bin/vasp2xyz.sh: /bin/bash^M: bad interpreter: No such file or directory
        
        I already put the file vasp2xyz.sh in bin folder,,,,how do you think Gowtham???
        
        GBU
      - Gowtham says:
        
        2010.01.22 at 21:30:28
        
        Ok – I think I know the problem. The error message says /bin/bash^M. ^M indicates invisible Carriage Return character. To get rid of them, do the following:
        
        1. vi $HOME/bin/vasp2xyz.sh
        
        2. :g/CTRL+V+M/s///g
        
        CTRL+V+M means hold down the Control Key along with V & M
        
        3. :wq
        
        4. Then try $HOME/bin/vasp2xyz.sh
        
        And let me know if this works.
Fendy says:

2010.01.22 at 21:56:10

Dear Gowtham

I try like you told me and I find something strange

[revival@localhost bin]$ vi $HOME/bin/vasp2xyz.sh

then I type :g/CTRL+V+M/s///g

Then I press my keyboard

And it says :

E486: Pattern not found: CTRL+V+M

Then I save it :wq

After that I try again

[revival@localhost bin]$ vasp2xyz.sh
bash: /home/revival/bin/vasp2xyz.sh: /bin/bash^M: bad interpreter: No such file or directory

for information,,,,,I’m using mandriva operating system,,,,I don’t know whether it always happens like this with mandriva

So Gowtham,,,,how do you think???

Thanks so much for helping a newbee like me

GBU

Reply
- Fendy says:
  
  2010.01.22 at 21:57:32
  
  O I miss type my reply
  
  “Then I press Enter on my keyboard”
  
  Sorry
  
  Reply
  - Gowtham says:
    
    2010.01.23 at 09:28:21
    
    CTRL+V+M means hold down the Control Key along with V & M
    
    Reply
    - Fendy says:
      
      2010.01.25 at 00:01:49
      
      Dear Gowtham
      
      I try it again
      
      I type g/CTRL+V+M/s///g
      
      CTRL+V+M means hold down the Control Key along with V & M
      and then I press Enter on my keyboard….This is the result :
      
      E486: Pattern not found: ^M
      
      So I save it again,,,,and then I type in command line
      
      [revival@localhost ~]$ $HOME/bin/vasp2xyz.sh
      bash: /home/revival/bin/vasp2xyz.sh: /bin/bash^M: bad interpreter: No such file or directory
      
      How do you think Gowtham???
      
      GBU
      
      Reply
      - Gowtham says:
        
        2010.01.25 at 07:25:05
        
        OK – the last trick in my bag is to try the following command:
        
        dos2unix $HOME/bin/vasp2xyz.sh
        
        and see if the command works.
        
        If not, then you are better off literally typing out the script.
      - Fendy says:
        
        2010.01.26 at 02:09:15
        
        Dear gowtham
        
        I’m sorry to tell you bad result,,,,it’s fail again,,,
        
        [revival@localhost ~]$ dos2unix $HOME/bin/vasp2xyz.sh
        bash: dos2unix: command not found
        
        Then I think I will need to type out the script by own,,,,anyway,,,,thanks so much for helping until now,,,,I appreciate all your kindness
        
        I will tell again the result
        
        GBU
handmade purses says:

2010.12.31 at 17:05:12

Why didn’t I consider about blogging about this topic? Fantastic job mate.

Reply
Latoyia Promisco says:

2012.01.04 at 08:10:35

It seemed that the freshmen RBs were still banged up. They give us the only shot to win (although wins against Tech and Kansas are really a joke). Without them we are fucked. That said, I think Case gives us the best shot to win on Tday. Ash is completely fucking lost. At least Case looks like he is trying.

Reply
Herb Laselle says:

2012.01.09 at 09:15:33

Hi, many thanks for this tutorial, but I still have a question.
After creating the actions for Index and going to any page other than the home page I get the page not found 404 error.

Reply

Most of these posts, especially the ones with any hint of technical jargon, are intended to be Note2Self. But if any of them float your boat, then feel free to sail along. If you feel so generous, improve my journey with your comments &/or thoughts!

Looking for MS Thesis or PhD Dissertation Template in LaTeX? Click below!

@NatGeoMag Just turned one in, taken last night in Houghton, Michigan #photos
# 4 hours ago

@realsteveshort Patriots' backup Center, Nick McDonald, is also a D2 rep from GVSU and Coach @DavidH51 knows him well! Go @NCAA DII
# 2012/02/06

@randal_sean Thank you - @Patriots faithful appreciate it :)
# 2012/02/06

BASH – vasp2xyz, A Script To Extract Coordinates From VASP

Test Case

Responses to BASH – vasp2xyz, A Script To Extract Coordinates From VASP

Leave a Reply

Archives