IDM

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Instructions

Before start, please read about the Improved Dimer Method [[1]].

1. Generate your initial guess for the structure (POSCAR). To this end, you can either pre-converge with a NEB calculation, or do it by hand.

2. Be sure the metal or solid phase is frozen and the molecule is relaxed. Do a frequency calculation based on your initial guess. Specify the following in your INCAR file:

frequencies:
  IBRION =   5     #     
  EDIFF  =  1E-7   # 
  POTIM  =   0.010 #                  
  NFREE  =   2     # 

3. Based on your POSCAR and OUTCAR of the frequencies calculation, generate in a new folder the input of the IDM with the getdimer script. For example:

getdimer ../freq/POSCAR ../freq/OUTCAR POSCAR

4. Specify the following in your INCAR file:

improved dimer method:
  IBRION =  44     # IDM    
  EDIFFG =  -0.015 # use force criteria
  POTIM  =   0.100 #                  
  NFREE  =   2     # 
  FINDIFF=   2     # 
  DIMER_DIST=0.010 #               
  MINROT =   0.010 # 
  STEP_SIZE= 0.010 #                
  STEP_MAX=  0.100 #                
  NSW    = 500     #  

Script and Executable

Instructions

1. Download the program Media:dimerdiag.tar. Extract it and put it in your ~/bin/exe/ folder

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

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

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

4. Now you can go to any folder and generate your dimer:

$ getdimer <input:POSCAR> <input:OUTCAR> <output:POSCAR>

SCRIPT

#!/bin/bash
# 
# Generates the POSCAR of a dimer calculation from the non mass-weighted Hessian matrix
# Rodrigo García-Muelas
# November 14th, 2014. Tarragona.
# 
# 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  [[  $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 -d ' ' -f3- 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

Alternative (old) versions

WARNING: Some of the topics discussed by David Karhánek are outdated. For instance, it is not necessary to set NWRITE=3 for the frequency calculation: IDM-IRC get-dimer-dir.sh get-irc-path.sh (by David Karhanek)

--Rgarcia 12:32, 18 November 2014 (CET)

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