Editing IBRION=3 bulk optimization

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= Procedure =

''See next section for the Script and Executable needed!''

To choose a proper value for the POTIM in case of a IBRION=3 bulk optimization

1. First you need to perform a frequency calculation, setting in the INCAR file
       
 frequencies:
  IBRION =   5     #     
  EDIFF  =  1E-7   # 
  POTIM  =   0.010 #                  
  NFREE  =   2     # 

  NWRITE =   3     #

'''PLEASE NOTE''': just the degrees of freedom of the investigated bonds must be relaxed. For instance in case of a Cu2O bulk relaxation, I relaxed two neighbour Cu atoms and the O in between.

2. When this calculation converge, based on the POSCAR and OUTCAR of the frequency calculation, you need to execute

 getdimer POSCAR OUTCAR POSCAR

which will generate a ''eigenvectors.dat'' file, presenting the following format

 Info:            0
 Eigenvalues
  -31.491683333336404       -29.378686935390292       -14.997850470930652       -9.6057143126896563       -5.4292953596452289       -1.6881155935524064       -1.3100285123688000       -1.1825456664410310      -0.59115181564548613 

3. Taken the highest eigenvalue, the proper POTIM is given, in this case, by

 1/31.491683333336404*0.7=0.0222280909

where 0.7 is set as a ''control parameter''.

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= Script and Executable needed =

''' Instructions '''

1. Download the program [[Image:dimerdiag.tgz]]. Extract it and put it in your ~/bin/exe/ folder

2. Copy the script in the ~/bin folder. Recommended name: getdimer. 

''''' SCRIPT '''''
 #!/bin/bash
 # 
 # Generates the POSCAR of a dimer calculation from the non mass-weighted Hessian matrix
 # Rodrigo García-Muelas
 # November 14th, 2014 - Created
 # March     9th, 2015 - Debugged 1 (Thanks to Marçal & Luca)
 # 
 # Use with VASP 5.x or higher
 # 
 # INPUT
 # $1 Path of the POSCAR file containing the coordinates
 # $2 Path of the OUTCAR file containing the frequencies of the structure
 # $3 <OUTPUT> POSCAR file
 # 
 
 # PART 0 - SECURITY CHECKS
 
 if [ -e $3 ] ; then
 echo "Warning! $3 already exist. Overwrite? (y/Y for yes)"
 read  overwrite
 case $overwrite in
 y|Y|Yes|yes|YES) echo "$3 will be overwriten"          ;;
 *)               echo "No actions taken "     ; exit 1 ;;
 esac
 fi
 
 IBRION=`grep IBRION $2 | awk '{print $3}'`
 if <tt><nowiki> [[ </nowiki></tt> $IBRION -gt "8" || $IBRION -lt "5" ]] ; then
 echo "$2 is not an OUTCAR of a frequency job."
 echo "No actions taken" ; exit 1 ; fi
 
 # PART 1 - READ POSCAR AND PREPARE INPUTS 
 
 cp $1 diagonalizer_poscar.tmp 
 
 # PART 2 - READ OUTCAR 
 
 grep "Degrees of freedom DOF " $2 > temp01.tmp
 freedom=`awk '{print $6}' temp01.tmp` 
 echo "$freedom" > diagonalizer_matrix.tmp
 
 grep -A $(($freedom+2)) 'SECOND DERIVATIVES' $2 > temp02.tmp
 cut -b 5- temp02.tmp > temp03.tmp
 tail -n $freedom temp03.tmp >> diagonalizer_matrix.tmp
 
 # PART 3 - DIAGONALIZE 
 /home/rgarcia/bin/exe/dimerdiag 
 
 # PART 4 - CLEAN
 head -n 9 $1 > $3
 cat    diagonalizer_taildm.tmp >> $3
 mv -f  diagonalizer_output.tmp eigenvectors.dat
 rm -fv *.tmp

3. Edit the script; change "rgarcia" by your username in this part:

 # PART 3 - DIAGONALIZE 
 /home/rgarcia/bin/exe/dimerdiag

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