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go back to [[Main Page]], [[Computational Resources]], [[Chemistry & More]], [[Computational Codes]], [[VASP]], [[Scripts for VASP]]
go back to [[Main Page]], [[Computational Resources]], [[Chemistry & More]], [[Computational Codes]], [[VASP]], [[Scripts for VASP]]


= Introduction =
= Instructions =


= Script =
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:


Please copy the following lines in your ~/bin folder. Recommended name: getdimer.  
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>
  $ getdimer <input:POSCAR> <input:OUTCAR> <output:POSCAR>
Example of use:
~/test/dimer$ getdimer ../freq/POSCAR ../freq/OUTCAR POSCAR


''''' SCRIPT '''''
''''' SCRIPT '''''
  #!/bin/bash
  #!/bin/bash
  #  
  #  
  # Generates the POSCAR of a dimer calculation
  # Generates the POSCAR of a dimer calculation from the non mass-weighted Hessian matrix
  # Rodrigo García-Muelas
  # Rodrigo García-Muelas
  # July 18th, 2014. Tarragona.
  # November 14th, 2014 - Created
# March    9th, 2015 - Debugged 1 (Thanks to Marçal & Luca)
  #  
  #  
  # Use with VASP 5.x or higher
  # Use with VASP 5.x or higher
Line 27: Line 68:
  # $2 Path of the OUTCAR file containing the frequencies of the structure
  # $2 Path of the OUTCAR file containing the frequencies of the structure
  # $3 <OUTPUT> POSCAR file
  # $3 <OUTPUT> POSCAR file
#
#
# Indexes
# a number of line
# b number of column
# c number of lattice vector, related to a
# d number of element, related to a
#
# VECTORS
# lattice
# element
# numelem
# coordin
  #  
  #  
   
   
  # PART 0 - SECURITY CHECKS
  # PART 0 - SECURITY CHECKS
   
   
  if [ -e $3 ] ; then  
  if [ -e $3 ] ; then
  echo "Warning! $3 already exist. Overwrite? (y/Y for yes)"
  echo "Warning! $3 already exist. Overwrite? (y/Y for yes)"
  read  overwrite
  read  overwrite
  case $overwrite in  
  case $overwrite in
  y|Y|Yes|yes|YES) echo "$3 will be overwriten"          ;;
  y|Y|Yes|yes|YES) echo "$3 will be overwriten"          ;;
  *)              echo "No actions taken "    ; exit 1 ;;
  *)              echo "No actions taken "    ; exit 1 ;;
  esac
  esac
  fi  
  fi
   
   
  IBRION=`grep IBRION $2 | awk '{print $3}'`
  IBRION=`grep IBRION $2 | awk '{print $3}'`
  if [[ $IBRION -gt "8" || $IBRION -lt "5" ]] ; then  
  if <tt><nowiki> [[ </nowiki></tt> $IBRION -gt "8" || $IBRION -lt "5" ]] ; then
  echo "$2 is not an OUTCAR of a frequency job."
  echo "$2 is not an OUTCAR of a frequency job."
  echo "No actions taken" ; exit 1 ; fi  
  echo "No actions taken" ; exit 1 ; fi
# PART 1 - READ POSCAR 
a=0
totalelem=0
totalatom=0
while read linea ; do  ##### 1 #####
a=$(($a+1)) ; b=0 ; d=$(($a-9)) ; line[$a]=$linea ;
# echo $a; #echo $line;  if [ $a -lt 10 ] ; then  echo "${line[$a]}" ;  fi
for word in ${line[$a]} ; do  ##### 2 #####
b=$(($b+1))
#if [ $a -lt 10 ] ; then echo "previous to case a is $a" ; fi
case $a in
1) title=${line[$a]} ;;
2) scaling=$word ;;
[3-5])  c=$(($a-2)) ; lattice[$c$b]=$word ;; #; echo "coordinates $c $b $word ${lattice[$c$b]}"
6) totalelem=$(($totalelem+1)) ; element[$b]=$word ;;
7) numelem[$b]=$word ; totalatom=$(($totalatom+$word))  ;;
8) selective=${line[$a]} ;;
9) directcartesian=${line[$a]} ;;
*) coord[$d$b]=$word ;; # echo "${coord[$d$b]}" ;;
esac
   
   
  #if [ $a -lt 10 ] ; then echo "word value is $word" ; fi
  # PART 1 - READ POSCAR AND PREPARE INPUTS
done ##### 2 #####
done < "$1"  ##### 1 #####
   
   
cp $1 diagonalizer_poscar.tmp
   
   
  # PART 2 - READ OUTCAR  
  # PART 2 - READ OUTCAR  
   
   
  grep -A $(($totalatom+1)) 'cm-1' OUTCAR > temp1.tmp
  grep "Degrees of freedom DOF " $2 > temp01.tmp
  tail -n $totalatom temp1.tmp | awk '{printf " %12.6f%12.6f%12.6f\n",$4,$5,$6}' > temp2.tmp
  freedom=`awk '{print $6}' temp01.tmp`
echo "$freedom" > diagonalizer_matrix.tmp
   
   
  # PART 3 - PRINT POSCAR  
  grep -A $(($freedom+2)) 'SECOND DERIVATIVES' $2 > temp02.tmp
  cut -b 5- temp02.tmp > temp03.tmp
tail -n $freedom temp03.tmp >> diagonalizer_matrix.tmp
   
   
  touch $3
  # PART 3 - DIAGONALIZE
echo "$title " >$3
  /home/rgarcia/bin/exe/dimerdiag
echo "$scaling " >>$3
echo "${lattice[11]}  ${lattice[12]}  ${lattice[13]} " >>$3
echo "${lattice[21]}  ${lattice[22]}  ${lattice[23]} " >>$3
echo "${lattice[31]}  ${lattice[32]}  ${lattice[33]} " >>$3
echo "${element[1]}  ${element[2]}  ${element[3]}  ${element[4]}  ${element[5]}  ${element[6]}  ${element[7]}  ${element[8]}  ${element[9]}  ${element[10]}  ${element[11]}  ${element[12]}  ${element[13]}  ${element[14]}  ${element[15]}  ${element[16]}  ${element[17]}  ${element[18]}  ${element[19]}  ${element[20]} " >>$3
echo "${numelem[1]}  ${numelem[2]}  ${numelem[3]}  ${numelem[4]}  ${numelem[5]}  ${numelem[6]}  ${numelem[7]}  ${numelem[8]}  ${numelem[9]}  ${numelem[10]}  ${numelem[11]}  ${numelem[12]}  ${numelem[13]}  ${numelem[14]}  ${numelem[15]}  ${numelem[16]}  ${numelem[17]}  ${numelem[18]}  ${numelem[19]}  ${numelem[20]} " >>$3
echo "$selective " >>$3
echo "$directcartesian " >>$3
d=0 ; until [ $d -eq $(($totalatom*10)) ] ; do d=$(($d+10)) ; echo "${coord[$(($d+1))]}  ${coord[$(($d+2))]}  ${coord[$(($d+3))]}  ${coord[$(($d+4))]}  ${coord[$(($d+5))]}  ${coord[$(($d+6))]}  " >>$3 ; done
  echo " " >>$3
   
   
  # PUT AS TAIL THE COORDINATES READ FROM THE OUTCAR
  # PART 4 - CLEAN
   
  head -n 9 $1 > $3
  cat temp2.tmp >> $3
  cat   diagonalizer_taildm.tmp >> $3
  echo ""      >> $3
  mv -f  diagonalizer_output.tmp eigenvectors.dat
  rm -f temp?.tmp
  rm -fv *.tmp


= Alternative (old) versions =
= Alternative (old) versions =


To see the other comments about the Improved Dimer Method, please see
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)


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-old]] [[get-dimer-dir.sh]] [[get-irc-path.sh]] (''by David Karhanek'')
go back to [[Main Page]], [[Computational Resources]], [[Chemistry & More]], [[Computational Codes]], [[VASP]], [[Scripts for VASP]]

Latest revision as of 18:20, 5 November 2019

go back to Main Page, Computational Resources, Chemistry & More, Computational Codes, VASP, Scripts for VASP

Instructions[edit]

Before start, please read about the Improved Dimer Method by Henkelman & Jónsson [1] and implemented in VASP by Heyden[2]. 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[edit]

Instructions

1. Download the program File: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  [[  $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[edit]

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)

go back to Main Page, Computational Resources, Chemistry & More, Computational Codes, VASP, Scripts for VASP

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