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Question Protected by Jamal
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200_success
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fixed copy-paste error in script
Source Link
Pierre
Pierre
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#!/bin/bash/

echo "LAMMPS file name? (without .lmps)"
read -r filename

# Make sure file exists
if [ -r "$filename".lmps ]; then

# Appends number of atoms to xyz file
head "$filename".lmps | grep atoms | awk -F' ' '{print $1}' > "$filename".xyz
echo >> "$filename".xyz

# Extracts "atom coordinates" and "masses" sections from original lmps file
awk '/Atoms/,/Bonds/' "$filename".lmps | head -n -2 | tail -n +3 > coordinates.tmp
awk '/Masses/,/Pair Coeffs/' "$filename".lmps | head -n -2 | tail -n +3 > masses.tmp

# Iterates over all lines of atom coordinates
while read line_atoms
do
    # Iterates over all lines of masses
    while read line_masses
    do
            mass=`echo $line_masses | awk -F' ' '{print $2}'`
            tag=`echo $line_masses | awk -F' ' '{print $1}'`

            case $mass in
                    # If mass corresponds to carbon and current line has lammps "carbon" tag
                    # then append this line to the xyz file 
                    12.011150)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "C\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;

                    # Same, checks for Hydrogen mass and lammps "hydrogen" tag
                    1.007970)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "H\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;
            esac
    done < masses.tmp

done < coordinates.tmp

# In case the requested file doesn't exist
else echo "Error:"$filename".lmps doesn't exits"

fi

# Gets rid of temporary files
rm *.tmp

#!/bin/bash/

# Appends number of atoms to xyz file
head "$filename".lmps | grep atoms | awk -F' ' '{print $1}' > "$filename".xyz
echo >> "$filename".xyz

# Extracts "atom coordinates" and "masses" sections from original lmps file
awk '/Atoms/,/Bonds/' "$filename".lmps | head -n -2 | tail -n +3 > coordinates.tmp
awk '/Masses/,/Pair Coeffs/' "$filename".lmps | head -n -2 | tail -n +3 > masses.tmp

# Iterates over all lines of atom coordinates
while read line_atoms
do
    # Iterates over all lines of masses
    while read line_masses
    do
            mass=`echo $line_masses | awk -F' ' '{print $2}'`
            tag=`echo $line_masses | awk -F' ' '{print $1}'`

            case $mass in
                    # If mass corresponds to carbon and current line has lammps "carbon" tag
                    # then append this line to the xyz file 
                    12.011150)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "C\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;

                    # Same, checks for Hydrogen mass and lammps "hydrogen" tag
                    1.007970)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "H\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;
            esac
    done < masses.tmp

done < coordinates.tmp

# In case the requested file doesn't exist
else echo "Error:"$filename".lmps doesn't exits"

fi

# Gets rid of temporary files
rm *.tmp

#!/bin/bash/

echo "LAMMPS file name? (without .lmps)"
read -r filename

# Make sure file exists
if [ -r "$filename".lmps ]; then

# Appends number of atoms to xyz file
head "$filename".lmps | grep atoms | awk -F' ' '{print $1}' > "$filename".xyz
echo >> "$filename".xyz

# Extracts "atom coordinates" and "masses" sections from original lmps file
awk '/Atoms/,/Bonds/' "$filename".lmps | head -n -2 | tail -n +3 > coordinates.tmp
awk '/Masses/,/Pair Coeffs/' "$filename".lmps | head -n -2 | tail -n +3 > masses.tmp

# Iterates over all lines of atom coordinates
while read line_atoms
do
    # Iterates over all lines of masses
    while read line_masses
    do
            mass=`echo $line_masses | awk -F' ' '{print $2}'`
            tag=`echo $line_masses | awk -F' ' '{print $1}'`

            case $mass in
                    # If mass corresponds to carbon and current line has lammps "carbon" tag
                    # then append this line to the xyz file 
                    12.011150)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "C\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;

                    # Same, checks for Hydrogen mass and lammps "hydrogen" tag
                    1.007970)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "H\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;
            esac
    done < masses.tmp

done < coordinates.tmp

# In case the requested file doesn't exist
else echo "Error:"$filename".lmps doesn't exits"

fi

# Gets rid of temporary files
rm *.tmp
added 147 characters in body; edited tags; edited title
Source Link
Jamal
Jamal
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  • 238

Advice needed for extracting Extracting data from text file in bash using awk, grep, head and tail

I've been writing bash script on and off, with pretty good results in terms of getting the job done. However, I'm worried that my script might be very ugly, as I am a beginner. So I'm I'm looking for advice concerning this particular one.

I want to extract some part of a big text file (here a lammps .lmps file), and manipulate it to create another file (here .xyz). The interesting parts of the big file are:

The beginninginteresting parts of the big file, are:

300 atoms
300 bonds
450 angles
600 dihedrals
150 impropers

The beginning of the file:

300 atoms
300 bonds
450 angles
600 dihedrals
150 impropers

theThe part about atom tag (here either "1" or "2") and mass,:

Masses

1         12.011150
2          1.007970

Pair Coeffs

Masses

1         12.011150
2          1.007970

Pair Coeffs

and theThe part concerning atom coordinates.:

Atoms

1       1    1     -0.126800     20.511864     28.359121     11.290877
2       1    1     -0.126800     21.779636     28.644716     10.779171
3       1    1     -0.126800     20.381316     27.822484     12.573717
4       1    1     -0.126800     21.518471     27.571445     13.344853
5       1    1     -0.126800     22.786244     27.857074     12.833161
6       1    1     -0.126800     22.916794     28.393694     11.550321
7       1    2      0.126800     19.390282     27.599170     12.973874
8       1    2      0.126800     19.622826     28.555315     10.688110
9       1    2      0.126800     23.907808     28.617021     11.150121
10      1    2      0.126800     21.881943     29.064261      9.776262
11      1    2      0.126800     23.675251     27.660865     13.435963
12      1    2      0.126800     21.416213     27.151893     14.347761

Bonds

Atoms

1       1    1     -0.126800     20.511864     28.359121     11.290877
2       1    1     -0.126800     21.779636     28.644716     10.779171
3       1    1     -0.126800     20.381316     27.822484     12.573717
4       1    1     -0.126800     21.518471     27.571445     13.344853
5       1    1     -0.126800     22.786244     27.857074     12.833161
6       1    1     -0.126800     22.916794     28.393694     11.550321
7       1    2      0.126800     19.390282     27.599170     12.973874
8       1    2      0.126800     19.622826     28.555315     10.688110
9       1    2      0.126800     23.907808     28.617021     11.150121
10      1    2      0.126800     21.881943     29.064261      9.776262
11      1    2      0.126800     23.675251     27.660865     13.435963
12      1    2      0.126800     21.416213     27.151893     14.347761

Bonds

#!/bin/bash/

# Appends number of atoms to xyz file
head "$filename".lmps | grep atoms | awk -F' ' '{print $1}' > "$filename".xyz
echo >> "$filename".xyz

# Extracts "atom coordinates" and "masses" sections from original lmps file
awk '/Atoms/,/Bonds/' "$filename".lmps | head -n -2 | tail -n +3 > coordinates.tmp
awk '/Masses/,/Pair Coeffs/' "$filename".lmps | head -n -2 | tail -n +3 > masses.tmp

# Iterates over all lines of atom coordinates
while read line_atoms
do
    # Iterates over all lines of masses
    while read line_masses
    do
            mass=`echo $line_masses | awk -F' ' '{print $2}'`
            tag=`echo $line_masses | awk -F' ' '{print $1}'`

            case $mass in
                    # If mass corresponds to carbon and current line has lammps "carbon" tag
                    # then append this line to the xyz file 
                    12.011150)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "C\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;

                    # Same, checks for Hydrogen mass and lammps "hydrogen" tag
                    1.007970)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "H\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;
            esac
    done < masses.tmp

done < coordinates.tmp

# In case the requested file doesn't exist
else echo "Error:"$filename".lmps doesn't exits"

fi

# Gets rid of temporary files
rm *.tmp

So the script works properly, and yields something like:

#!/bin/bash/

# Appends number of atoms to xyz file
head "$filename".lmps | grep atoms | awk -F' ' '{print $1}' > "$filename".xyz
echo >> "$filename".xyz

# Extracts "atom coordinates" and "masses" sections from original lmps file
awk '/Atoms/,/Bonds/' "$filename".lmps | head -n -2 | tail -n +3 > coordinates.tmp
awk '/Masses/,/Pair Coeffs/' "$filename".lmps | head -n -2 | tail -n +3 > masses.tmp

# Iterates over all lines of atom coordinates
while read line_atoms
do
    # Iterates over all lines of masses
    while read line_masses
    do
            mass=`echo $line_masses | awk -F' ' '{print $2}'`
            tag=`echo $line_masses | awk -F' ' '{print $1}'`

            case $mass in
                    # If mass corresponds to carbon and current line has lammps "carbon" tag
                    # then append this line to the xyz file 
                    12.011150)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "C\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;

                    # Same, checks for Hydrogen mass and lammps "hydrogen" tag
                    1.007970)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "H\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;
            esac
    done < masses.tmp

done < coordinates.tmp

# In case the requested file doesn't exist
else echo "Error:"$filename".lmps doesn't exits"

fi

# Gets rid of temporary files
rm *.tmp

300

C       20.511864        28.359121       11.290877
C       21.779636        28.644716       10.779171
C       20.381316        27.822484       12.573717
C       21.518471        27.571445       13.344853
C       22.786244        27.857074       12.833161
C       22.916794        28.393694       11.550321
H       19.390282        27.599170       12.973874
H       19.622826        28.555315       10.688110
H       23.907808        28.617021       11.150121
H       21.881943        29.064261       9.776262
H       23.675251        27.660865       13.435963
H       21.416213        27.151893       14.347761

The script works properly, and yields something like:

300

C       20.511864        28.359121       11.290877
C       21.779636        28.644716       10.779171
C       20.381316        27.822484       12.573717
C       21.518471        27.571445       13.344853
C       22.786244        27.857074       12.833161
C       22.916794        28.393694       11.550321
H       19.390282        27.599170       12.973874
H       19.622826        28.555315       10.688110
H       23.907808        28.617021       11.150121
H       21.881943        29.064261       9.776262
H       23.675251        27.660865       13.435963
H       21.416213        27.151893       14.347761

Thanks in advance for your time :)

Advice needed for extracting data from text file in bash using awk, grep, head and tail

I've been writing bash script on and off, with pretty good results in terms of getting the job done. However, I'm worried that my script might be very ugly, as I am a beginner. So I'm looking for advice concerning this particular one.

I want to extract some part of a big text file (here a lammps .lmps file), and manipulate it to create another file (here .xyz). The interesting parts of the big file are:

The beginning of the file,

300 atoms
300 bonds
450 angles
600 dihedrals
150 impropers

the part about atom tag (here either "1" or "2") and mass,

Masses

1         12.011150
2          1.007970

Pair Coeffs

and the part concerning atom coordinates.

Atoms

1       1    1     -0.126800     20.511864     28.359121     11.290877
2       1    1     -0.126800     21.779636     28.644716     10.779171
3       1    1     -0.126800     20.381316     27.822484     12.573717
4       1    1     -0.126800     21.518471     27.571445     13.344853
5       1    1     -0.126800     22.786244     27.857074     12.833161
6       1    1     -0.126800     22.916794     28.393694     11.550321
7       1    2      0.126800     19.390282     27.599170     12.973874
8       1    2      0.126800     19.622826     28.555315     10.688110
9       1    2      0.126800     23.907808     28.617021     11.150121
10      1    2      0.126800     21.881943     29.064261      9.776262
11      1    2      0.126800     23.675251     27.660865     13.435963
12      1    2      0.126800     21.416213     27.151893     14.347761

Bonds

#!/bin/bash/

# Appends number of atoms to xyz file
head "$filename".lmps | grep atoms | awk -F' ' '{print $1}' > "$filename".xyz
echo >> "$filename".xyz

# Extracts "atom coordinates" and "masses" sections from original lmps file
awk '/Atoms/,/Bonds/' "$filename".lmps | head -n -2 | tail -n +3 > coordinates.tmp
awk '/Masses/,/Pair Coeffs/' "$filename".lmps | head -n -2 | tail -n +3 > masses.tmp

# Iterates over all lines of atom coordinates
while read line_atoms
do
    # Iterates over all lines of masses
    while read line_masses
    do
            mass=`echo $line_masses | awk -F' ' '{print $2}'`
            tag=`echo $line_masses | awk -F' ' '{print $1}'`

            case $mass in
                    # If mass corresponds to carbon and current line has lammps "carbon" tag
                    # then append this line to the xyz file 
                    12.011150)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "C\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;

                    # Same, checks for Hydrogen mass and lammps "hydrogen" tag
                    1.007970)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "H\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;
            esac
    done < masses.tmp

done < coordinates.tmp

# In case the requested file doesn't exist
else echo "Error:"$filename".lmps doesn't exits"

fi

# Gets rid of temporary files
rm *.tmp

So the script works properly, and yields something like:

300

C       20.511864        28.359121       11.290877
C       21.779636        28.644716       10.779171
C       20.381316        27.822484       12.573717
C       21.518471        27.571445       13.344853
C       22.786244        27.857074       12.833161
C       22.916794        28.393694       11.550321
H       19.390282        27.599170       12.973874
H       19.622826        28.555315       10.688110
H       23.907808        28.617021       11.150121
H       21.881943        29.064261       9.776262
H       23.675251        27.660865       13.435963
H       21.416213        27.151893       14.347761

Thanks in advance for your time :)

Extracting data from text file in bash using awk, grep, head and tail

I've been writing bash script on and off, with pretty good results in terms of getting the job done. However, I'm worried that my script might be very ugly, as I am a beginner. I'm looking for advice concerning this particular one.

I want to extract some part of a big text file (here a lammps .lmps file), and manipulate it to create another file (here .xyz).

The interesting parts of the big file are:

The beginning of the file:

300 atoms
300 bonds
450 angles
600 dihedrals
150 impropers

The part about atom tag (here either "1" or "2") and mass:

Masses

1         12.011150
2          1.007970

Pair Coeffs

The part concerning atom coordinates:

Atoms

1       1    1     -0.126800     20.511864     28.359121     11.290877
2       1    1     -0.126800     21.779636     28.644716     10.779171
3       1    1     -0.126800     20.381316     27.822484     12.573717
4       1    1     -0.126800     21.518471     27.571445     13.344853
5       1    1     -0.126800     22.786244     27.857074     12.833161
6       1    1     -0.126800     22.916794     28.393694     11.550321
7       1    2      0.126800     19.390282     27.599170     12.973874
8       1    2      0.126800     19.622826     28.555315     10.688110
9       1    2      0.126800     23.907808     28.617021     11.150121
10      1    2      0.126800     21.881943     29.064261      9.776262
11      1    2      0.126800     23.675251     27.660865     13.435963
12      1    2      0.126800     21.416213     27.151893     14.347761

Bonds

#!/bin/bash/

# Appends number of atoms to xyz file
head "$filename".lmps | grep atoms | awk -F' ' '{print $1}' > "$filename".xyz
echo >> "$filename".xyz

# Extracts "atom coordinates" and "masses" sections from original lmps file
awk '/Atoms/,/Bonds/' "$filename".lmps | head -n -2 | tail -n +3 > coordinates.tmp
awk '/Masses/,/Pair Coeffs/' "$filename".lmps | head -n -2 | tail -n +3 > masses.tmp

# Iterates over all lines of atom coordinates
while read line_atoms
do
    # Iterates over all lines of masses
    while read line_masses
    do
            mass=`echo $line_masses | awk -F' ' '{print $2}'`
            tag=`echo $line_masses | awk -F' ' '{print $1}'`

            case $mass in
                    # If mass corresponds to carbon and current line has lammps "carbon" tag
                    # then append this line to the xyz file 
                    12.011150)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "C\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;

                    # Same, checks for Hydrogen mass and lammps "hydrogen" tag
                    1.007970)
                    if [ "$tag" == `echo $line_atoms | awk -F' ' '{print $3}'` ]; then
                    echo -e "H\t`echo $line_atoms | awk -F' ' '{print $5,"\t",$6,"\t",$7}'`" >> "$filename".xyz
                    fi
                    ;;
            esac
    done < masses.tmp

done < coordinates.tmp

# In case the requested file doesn't exist
else echo "Error:"$filename".lmps doesn't exits"

fi

# Gets rid of temporary files
rm *.tmp

The script works properly, and yields something like:

300

C       20.511864        28.359121       11.290877
C       21.779636        28.644716       10.779171
C       20.381316        27.822484       12.573717
C       21.518471        27.571445       13.344853
C       22.786244        27.857074       12.833161
C       22.916794        28.393694       11.550321
H       19.390282        27.599170       12.973874
H       19.622826        28.555315       10.688110
H       23.907808        28.617021       11.150121
H       21.881943        29.064261       9.776262
H       23.675251        27.660865       13.435963
H       21.416213        27.151893       14.347761
Source Link
Pierre
Pierre
  • 103
  • 1
  • 1
  • 6