Editing IDM

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= Instructions =

Before start, please read about the Improved Dimer Method by Henkelman & Jónsson [https://aip.scitation.org/doi/10.1063/1.480097] and implemented in VASP by Heyden[http://dx.doi.org/10.1063/1.2104507]. Then kindly follow the procedures detailed here: 

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-6   # 
   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    
   EDIFF  =   1E-6  # 
   EDIFFG =  -0.030 # use force criteria
   POTIM  =   0.050 # Between 0.010 and 0.100.                  
   NFREE  =   2     # Between 2&5
   FINDIFF=   2     # 
   DIMER_DIST=0.010 #               
   MINROT =   0.010 # 
   STEP_SIZE= 0.010 #                
   STEP_MAX=  0.100 #                
   NSW    = 100     # Never use more than 200. Check periodically for divergence.

5. To check that it is converging well, (1) check with p4vasp that all forces are small, and (2) check that the curvature is always negative. Normal values are between -1.0 and -30.0:
 grep curv OUTCAR

= Script and Executable =

''' 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. 

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 - 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

= 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'')

--[[User:Rgarcia|Rgarcia]] 12:32, 18 November 2014 (CET)

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