Shell-Scripting-1.pdf

Shell Scripting
Alexander B. Pacheco
LTS Research Computing

Outline
1 Introduction
Types of Shell
Variables
File Permissions
Input and Output
2 Shell Scripting
Getting Started with Writing Simple Scripts
Arithmetic Operations
Flow Control
Arrays
Command Line Arguments
Functions
3 Unix Utilities
grep
sed
4 awk programming
5 Wrap Up
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Introduction
What is a SHELL
The command line interface is the primary interface to Linux/Unix operating systems.
Shells are how command-line interfaces are implemented in Linux/Unix.
Each shell has varying capabilities and features and the user should choose the shell
that best suits their needs.
The shell is simply an application running on top of the kernel and provides a powerful
interface to the system.
Other Software
Shell
Kernel
H
a
rdw
a
r
e
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Types of Shell
sh : Bourne Shell
Developed by Stephen Bourne at ATT Bell Labs
csh : C Shell
Developed by Bill Joy at University of California, Berkeley
ksh : Korn Shell
Developed by David Korn at ATT Bell Labs
backward-compatible with the Bourne shell and includes many features of the C
shell
bash : Bourne Again Shell
Developed by Brian Fox for the GNU Project as a free software replacement for
the Bourne shell (sh).
Default Shell on Linux and Mac OSX
The name is also descriptive of what it did, bashing together the features of sh,
csh and ksh
tcsh : TENEX C Shell
Developed by Ken Greer at Carnegie Mellon University
It is essentially the C shell with programmable command line completion,
command-line editing, and a few other features.
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Shell Comparison
sh csh ksh bash tcsh
Programming Language 3 3 3 3 3
Shell Variables 3 3 3 3 3
Command alias 7 3 3 3 3
Command history 7 3 3 3 3
Filename completion 7 M M 3 3
Command line editing 7 7 M 3 3
Job control 7 3 3 3 3
3 : Yes
7 : No
M : Yes, not set by default
http://www.cis.rit.edu/class/simg211/unixintro/Shell.html
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Variables I
A variable is a named object that contains data used by one or more applications.
There are two types of variables, Environment and User Defined and can contain a
number, character or a string of characters.
Environment Variables provides a simple way to share configuration settings between
multiple applications and processes in Linux.
As in programming languages like C, C++ and Fortran, defining your own variables
makes the program or script extensible by you or a third party
Rules for Variable Names
1 Variable names must start with a letter or underscore
2 Number can be used anywhere else
3 DO NOT USE special characters such as @, #, %, $
4 Case sensitive
5 Examples
Allowed: VARIABLE, VAR1234able, var name, VAR
Not Allowed: 1VARIABLE, %NAME, $myvar, VAR@NAME
To reference a variable, environment or user defined, you need to prepend the variable
name with ”$” as in $VARIABLE, $PATH, etc.
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Variables II
Its a good practice to protect your variable name within {. . . } such as ${PATH} when
referencing it. (We’ll see an example in a few slides)
Assigning value to a variable
Type sh,ksh,bash csh,tcsh
Shell name=value set name = value
Environment export name=value setenv name value
sh,ksh,bash THERE IS NO SPACE ON EITHER SIDE OF =
csh,tcsh space on either side of = is allowed for the set command
csh,tcsh There is no = in the setenv command
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File Permissions I
In *NIX OS’s, you have three types of file permissions
1 read (r)
2 write (w)
3 execute (x)
for three types of users
1 user
2 group
3 world i.e. everyone else who has access to the system
drwxr-xr-x. 2 user user 4096 Jan 28 08:27 Public
-rw-rw-r- -. 1 user user 3047 Jan 28 09:34 README
The first character signifies the type of the file
d for directory
l for symbolic link
- for normal file
The next three characters of first triad signifies what the owner can do
The second triad signifies what group member can do
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File Permissions II
The third triad signifies what everyone else can do
d rwx
|{z}
u
g
z }| {
r − x r − x
| {z }
o
Read carries a weight of 4
Write carries a weight of 2
Execute carries a weight of 1
The weights are added to give a value of 7 (rwx), 6(rw), 5(rx) or 3(wx) permissions.
chmod is a *NIX command to change permissions on a file
To give user rwx, group rx and world x permission, the command is
chmod 751 filename
Instead of using numerical permissions you can also use symbolic mode
u/g/o or a user/group/world or all i.e. ugo
+/- Add/remove permission
r/w/x read/write/execute
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File Permissions III
Give everyone execute permission:
chmod a+x hello.sh
chmod ugo+x hello.sh
Remove group and world read write permission:
chmod go-rw hello.sh
Use the -R flag to change permissions recursively, all files and directories and their
contents.
chmod -R 755 ${HOME}/*
What is the permission on ${HOME}?
HPC Users
If you want to share your files with your colleagues
1 Make your home directory read accessible to the world
chmod 755 ${HOME}
do not use the recursive -R flag
2 Change to your home directory and give read access to the directory that you want to
share using the -R flag
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Input/Output I
For reading input from screen/keyboard/prompt
bash read
tcsh $
The read statement takes all characters typed until the Enter key is pressed and
stores them into a variable.
Syntax read variable name
Example read name Enter
Alex Pacheco
$ can accept only one argument. If you have multiple arguments, enclose the $
within quotes e.g. $
Syntax: set variable = $
Example: set name = $ Enter
Alex Pacheco
In the above examples, the name that you enter in stored in the variable name.
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Input/Output II
The command echo is used for displaying output to screen
Use the echo command to print the variable name to the screen
echo $name Enter
The echo statement can print multiple arguments.
By default, echo eliminates redundant whitespace (multiple spaces and tabs) and
replaces it with a single whitespace between arguments.
To include redundant whitespace, enclose the arguments within double quotes
echo Welcome to HPC Training (more than one space between HPC and
Training)
echo Welcome to HPC Training
read name or set name = $
Alex Pacheco
echo $name
echo $name
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Input/Output III
You can also use the printf command to display output
Syntax: printf format arguments
Example: printf $name
printf %sn $name
Format Descriptors
%s print argument as a string
%d print argument as an integer
%f print argument as a floating point number
n print new line
you can add a width for the argument between the % and {s,d,f} fields
%4s, %5d, %7.4f
The printf command is used in awk to print formatted data (more on this later)
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I/O Redirection
There are three file descriptors for I/O streams
1 STDIN: Standard Input
2 STDOUT: Standard Output
3 STDERR: Standard Error
1 represents STDOUT and 2 represents STDERR
I/O redirection allows users to connect applications
: connects a file to STDIN of an application
: connects STDOUT of an application to a file
: connects STDOUT of an application by appending to a file
| : connects the STDOUT of an application to STDIN of another application.
Examples:
1 write STDOUT to file: ls -l ls-l.out
2 write STDERR to file: ls -l 2 ls-l.err
3 write STDOUT to STDERR: ls -l 12
4 write STDERR to STDOUT: ls -l 21
5 send STDOUT as STDIN: ls -l | wc -l
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What is a scripting language?
A scripting language or script language is a programming language that supports
the writing of scripts.
Scripting Languages provide a higher level of abstraction than standard
programming languages.
Compared to programming languages, scripting languages do not distinguish between
data types: integers, real values, strings, etc.
Scripting Languages tend to be good for automating the execution of other programs.
analyzing data
running daily backups
They are also good for writing a program that is going to be used only once and then
discarded.
A script is a program written for a software environment that automate the execution
of tasks which could alternatively be executed one-by-one by a human operator.
The majority of script programs are “quick and dirty”, where the main goal is to get
the program written quickly.
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Writing your first script
Three things to do to write and execute a script
1 Write a script
A shell script is a file that contains ASCII text.
Create a file, hello.sh with the following lines
#!/bin/bash
# My First Script
echo Hello World!
2 Set permissions
~/Tutorials/BASH/scripts chmod 755 hello.sh
OR
~/Tutorials/BASH/scripts chmod a+x hello.sh
3 Execute the script
~/Tutorials/BASH/scripts ./hello.sh
Hello World!
4 If you do not set execute permission for the script, then
~/Tutorials/BASH/scripts sh hello.sh
Hello World!
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Description of the script
My First Script
#!/bin/bash
# My First Script
echo Hello World!
The first line is called the ”ShaBang” line. It tells the OS which interpreter to use. In
the current example, bash
Other options are:
sh : #!/bin/sh
ksh : #!/bin/ksh
csh : #!/bin/csh
tcsh: #!/bin/tcsh
The second line is a comment. All comments begin with ”#”.
The third line tells the OS to print ”Hello World!” to the screen.
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Special Characters
#: starts a comment.
$: indicates the name of a variable.
: escape character to display next character literally.
{ }: used to enclose name of variable.
; Command separator [semicolon]. Permits putting two or more commands
on the same line.
;; Terminator in a case option [double semicolon].
. ”dot” command [period]. Equivalent to source. This is a bash builtin.
$? exit status variable.
$$ process ID variable.
[ ] test expression
[[ ]] test expression, more flexible than [ ]
$[ ], (( )) integer expansion
||, , ! Logical OR, AND and NOT
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Quotation
Double Quotation
Enclosed string is expanded (”$”, ”/” and ”‘”)
Example: echo $myvar prints the value of myvar
Single Quotation ’ ’
Enclosed string is read literally
Example: echo ’$myvar’ prints $myvar
Back Quotation ‘ ‘
Used for command substitution
Enclosed string is executed as a command
Example: echo ‘pwd‘ prints the output of the pwd command i.e. print working
directory
In bash, you can also use $(· · · ) instead of ‘· · · ‘
e.g. $(pwd) and ‘pwd‘ are the same
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Example
#!/bin/bash
HI=Hello
echo HI # displays HI
echo $HI # displays Hello
echo $HI # displays $HI
echo $HI # displays Hello
echo ’$HI ’ # displays $HI
echo $HIAlex # displays nothing
echo ${HI}Alex # displays HelloAlex
echo ‘pwd ‘ # displays working directory
echo $(pwd) # displays working directory
~/Tutorials/BASH/scripts/day1/examples ./quotes.sh
HI
Hello
$HI
Hello
$HI
HelloAlex
/home/apacheco/Tutorials/BASH/scripts/day1/examples
/home/apacheco/Tutorials/BASH/scripts/day1/examples
~/Tutorials/BASH/scripts/day1/examples
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Arithmetic Operations I
You can carry out numeric operations on integer variables
Operation Operator
Addition +
Subtraction -
Multiplication *
Division /
Exponentiation ** (bash only)
Modulo %
Arithmetic operations in bash can be done within the $((· · · )) or $[· · · ] commands
F Add two numbers: $((1+2))
F Multiply two numbers: $[$a*$b]
F You can also use the let command: let c=$a-$b
F or use the expr command: c=‘expr $a - $b‘
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Arithmetic Operations II
In tcsh,
F Add two numbers: @ x = 1 + 2
F Divide two numbers: @ x = $a / $b
F You can also use the expr command: set c = ‘expr $a % $b‘
Note the use of space
bash space required around operator in the expr command
tcsh space required between @ and variable, around = and numeric operators.
You can also use C-style increment operators
bash let c+=1 or let c--
tcsh @ x -= 1 or @ x++
/=, *= and %= are also allowed.
bash
The above examples only work for integers.
What about floating point number?
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Arithmetic Operations III
Using floating point in bash or tcsh scripts requires an external calculator like GNU
bc.
F Add two numbers:
echo 3.8 + 4.2 | bc
F Divide two numbers and print result with a precision of 5 digits:
echo scale=5; 2/5 | bc
F Call bc directly:
bc scale=5; 2/5
F Use bc -l to see result in floating point at max scale:
bc -l 2/5
You can also use awk for floating point arithmetic.
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Flow Control
Shell Scripting Languages execute commands in sequence similar to programming
languages such as C, Fortran, etc.
Control constructs can change the sequential order of commands.
Control constructs available in bash and tcsh are
1 Conditionals: if
2 Loops: for, while, until
3 Switches: case, switch
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if statement
An if/then construct tests whether the exit status of a list of commands is 0, and if
so, executes one or more commands.
bash
if [ condition1 ]; then
some commands
elif [ condition2 ]; then
some commands
else
some commands
fi
tcsh
if ( condition1 ) then
some commands
else if ( condition2 ) then
some commands
else
some commands
endif
Note the space between condition and ”[” ”]”
bash is very strict about spaces.
tcsh commands are not so strict about spaces.
tcsh uses the if-then-else if-else-endif similar to Fortran.
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Comparison Operators
Integer Comparison
Operation bash tcsh
equal to if [ 1 -eq 2 ] if (1 == 2)
not equal to if [ $a -ne $b ] if ($a != $b)
greater than if [ $a -gt $b ] if ($a $b)
greater than or equal to if [ 1 -ge $b ] if (1 = $b)
less than if [ $a -lt 2 ] if ($a 2)
less than or equal to if [ $a -le $b ] if ($a = $b)
String Comparison
operation bash tcsh
equal to if [ $a == $b ] if ($a == $b)
not equal to if [ $a != $b ] if ($a != $b)
zero length or null if [ -z $a ] if ($%a == 0)
non zero length if [ -n $a ] if ($%a 0)
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File Test Logical Operators
File Test Operators
Operation bash tcsh
file exists if [ -e .bashrc ] if ( -e .tcshrc )
file is a regular file if [ -f .bashrc ]
file is a directory if [ -d /home ] if ( -d /home )
file is not zero size if [ -s .bashrc ] if ( ! -z .tcshrc)
file has read permission if [ -r .bashrc ] if ( -r .tcshrc)
file has write permission if [ -w .bashrc ] if ( -w .tcshrc)
file has execute permission if [ -x .bashrc ] if ( -x .tcshrc)
Logical Operators
Operation bash tcsh
Operation bash tcsh
NOT if [ ! -e .bashrc ] if ( ! -z .tcshrc)
AND if [ $a -eq 2 ] [ $x -gt $y ] if ($a == 2 $x = $y )
OR if [[ $a -eq 2 || $x -gt $y ]] if ($a == 2 || $x = $y )
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Examples
Condition tests using the if/then may be nested
read a
if [ $a -gt 0 ]; then
if [ $a -lt 5 ]; then
echo The value of a lies somewhere between 0
and 5
fi
fi
set a = $
if ( $a 0 ) then
if ( $a 5 ) then
echo The value of $a lies somewhere between
0 and 5
endif
endif
This is same as
read a
if [[ $a -gt 0 $a -lt 5 ]]; then
echo The value of $a lies somewhere between 0 and
5
fi
OR
if [ $a -gt 0 ] [ $a -lt 5 ]; then
echo The value of $a lies somewhere between 0 and
5
fi
set a = $
if ( $a 0 $a 5 ) then
echo The value of $a lies somewhere between 0
and 5
endif
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Loop Constructs
A loop is a block of code that iterates a list of commands as long as the loop control
condition is true.
Loop constructs available in
bash: for, while and until
tcsh: foreach and while
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bash: for loops
The for loop is the basic looping construct in bash
for arg in list
do
some commands
done
the for and do lines can be written on the same line: for arg in list; do
for loops can also use C style syntax
for (( EXP1; EXP2; EXP3 )); do
some commands
done
for i in $(seq 1 10)
do
touch file${i}. dat
done
for i in $(seq 1 10); do
touch file${i}. dat
done
for ((i=1;i =10;i++))
do
touch file${i}. dat
done
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tcsh: foreach loop
The foreach loop is the basic looping construct in tcsh
foreach arg (list)
some commands
end
foreach i (‘seq 1 10‘)
touch file$i.dat
end
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while Construct
The while construct tests for a condition at the top of a loop, and keeps looping as
long as that condition is true (returns a 0 exit status).
In contrast to a for loop, a while loop finds use in situations where the number of loop
repetitions is not known beforehand.
bash
while [ condition ]
do
some commands
done
tcsh
while ( condition )
some commands
end
factorial.sh
#!/bin/bash
echo -n Enter a number less than 10:
read counter
factorial =1
while [ $counter -gt 0 ]
do
factorial=$(( $factorial * $counter ))
counter=$(( $counter - 1 ))
done
echo $factorial
factorial.csh
#!/bin/tcsh
set counter = $
set factorial = 1
while ( $counter 0 )
@ factorial = $factorial * $counter
@ counter -= 1
end
echo $factorial
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until Contruct (bash only)
The until construct tests for a condition at the top of a loop, and keeps looping as
long as that condition is false (opposite of while loop).
until [ condition is true ]
do
some commands
done
factorial2.sh
#!/bin/bash
read counter
factorial =1
until [ $counter -le 1 ]; do
factorial=$[ $factorial * $counter ]
if [ $counter -eq 2 ]; then
break
else
let counter -=2
fi
done
echo $factorial
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Nested Loops
for, while until loops can nested. To exit from the loop use the break command
nestedloops.sh
#!/bin/bash
## Example of Nested loops
echo Nested for loops
for a in $(seq 1 5) ; do
echo Value of a in outer loop: $a
for b in ‘seq 1 2 5‘ ; do
c=$(($a*$b))
if [ $c -lt 10 ]; then
echo a * b = $a * $b = $c
else
echo $a * $b 10
break
fi
done
done
echo ========================
echo
echo Nested for and while loops
for ((a=1;a =5;a++)); do
b=1
while [ $b -le 5 ]; do
c=$(($a*$b))
if [ $c -lt 5 ]; then
echo a * b = $a * $b = $c
else
echo $a * $b 5
break
fi
let b+=2
done
done
echo ========================
nestedloops.csh
#!/bin/tcsh
## Example of Nested loops
echo Nested for loops
foreach a (‘seq 1 5‘)
foreach b (‘seq 1 2 5‘)
@ c = $a * $b
if ( $c 10 ) then
echo a * b = $a * $b = $c
else
echo $a * $b 10
break
endif
end
end
echo ========================
echo
echo Nested for and while loops
foreach a (‘seq 1 5‘)
set b = 1
while ( $b = 5 )
@ c = $a * $b
if ( $c 5 ) then
echo a * b = $a * $b = $c
else
echo $a * $b 5
break
endif
@ b = $b + 2
end
end
echo ========================
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Switching or Branching Constructs I
The case and select constructs are technically not loops, since they do not iterate the
execution of a code block.
Like loops, however, they direct program flow according to conditions at the top or bottom
of the block.
case construct
case variable in
condition1)
some command
;;
condition2)
some other command
;;
esac
select construct
select variable [ list ]
do
command
break
done
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Switching or Branching Constructs II
tcsh has the switch construct
switch construct
switch (arg list)
case variable
some command
breaksw
endsw
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dooper.sh
#!/bin/bash
echo Print two numbers
read num1 num2
echo What operation do you want to do?
operations=’add subtract multiply divide exponentiate
modulo all quit ’
select oper in $operations ; do
case $oper in
add)
echo $num1 + $num2 = $[$num1 + $num2]
;;
subtract)
echo $num1 - $num2 = $[$num1 - $num2]
;;
multiply)
echo $num1 * $num2 = $[$num1 * $num2]
;;
exponentiate )
echo $num1 ** $num2 = $[$num1 ** $num2]
;;
divide)
echo $num1 / $num2 = $[$num1 / $num2]
;;
modulo)
echo $num1 % $num2 = $[$num1 % $num2]
;;
all)
;;
*)
exit
;;
esac
done
dooper.csh
#!/bin/tcsh
echo Print two numbers one at a time
set num1 = $
set num2 = $
echo Enter +, -, x, /, % or all
set oper = $
switch ( $oper )
case x
@ prod = $num1 * $num2
echo $num1 * $num2 = $prod
breaksw
case all
@ sum = $num1 + $num2
echo $num1 + $num2 = $sum
@ diff = $num1 - $num2
echo $num1 - $num2 = $diff
@ prod = $num1 * $num2
echo $num1 * $num2 = $prod
@ ratio = $num1 / $num2
echo $num1 / $num2 = $ratio
@ remain = $num1 % $num2
echo $num1 % $num2 = $remain
breaksw
case *
@ result = $num1 $oper $num2
echo $num1 $oper $num2 = $result
breaksw
endsw
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~/Tutorials/BASH/scripts ./day1/examples/dooper.sh
Print two numbers
1 4
What operation do you want to do?
1) add 3) multiply 5) exponentiate 7) all
2) subtract 4) divide 6) modulo 8) quit
#? 7
1 + 4 = 5
1 - 4 = -3
1 * 4 = 4
1 ** 4 = 1
1 / 4 = 0
1 % 4 = 1
#? 8
~/Tutorials/BASH/scripts ./day1/examples/dooper.csh
Print two numbers one at a time
1
5
Enter +, -, x, /, % or all
all
1 + 5 = 6
1 - 5 = -4
1 * 5 = 5
1 / 5 = 0
1 % 5 = 1
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dooper1.sh
#!/bin/bash
echo Print two numbers
read num1 num2
echo Options are add , subtract , multiply ,
exponentiate , divide , modulo and all
read oper
case $oper in
add)
;;
subtract)
;;
multiply)
;;
exponentiate )
;;
divide)
;;
modulo)
;;
all)
;;
*)
exit
;;
esac
~/Tutorials/BASH/scripts ./day1/examples/dooper1.sh
Print two numbers
2 5
Options are add , subtract , multiply , exponentiate ,
divide , modulo and all
all
2 + 5 = 7
2 - 5 = -3
2 * 5 = 10
2 ** 5 = 32
2 / 5 = 0
2 % 5 = 2
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Arrays I
bash and tcsh supports one-dimensional arrays.
Array elements may be initialized with the variable[xx] notation
variable[xx]=1
Initialize an array during declaration
bash name=(firstname ’last name’)
tcsh set name = (firstname ’last name’)
reference an element i of an array name
${name[i]}
print the whole array
bash ${name[@]}
tcsh ${name}
print length of array
bash ${#name[@]}
tcsh ${#name}
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Arrays II
print length of element i of array name
${#name[i]}
Note: In bash ${#name} prints the length of the first element of the array
Add an element to an existing array
bash name=(title ${name[@]})
tcsh set name = ( title ${name})
In tcsh everything within ”...” is one variable.
In the above tcsh example, title is first element of new array while the second
element is the old array name
copy an array name to an array user
bash user=(${name[@]})
tcsh set user = ( ${name} )
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Arrays III
concatenate two arrays
bash nameuser=(${name[@]} ${user[@]})
tcsh set nameuser=( ${name} ${user} )
delete an entire array
unset name
remove an element i from an array
bash unset name[i]
tcsh @ j = $i - 1
@ k =$i + 1
set name = ( ${name[1-$j]} ${name[$k-]})
bash the first array index is zero (0)
tcsh the first array index is one (1)
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Arrays IV
name.sh
#!/bin/bash
echo Print your first and last name
read firstname lastname
name =( $firstname $lastname)
echo Hello ${name[@]}
echo Enter your salutation
read title
echo Enter your suffix
read suffix
name =( $title ${name[@]} $suffix)
unset name [2]
name.csh
#!/bin/tcsh
echo Print your first name
set firstname = $
echo Print your last name
set lastname = $
set name = ( $firstname $lastname)
echo Hello ${name}
echo Enter your salutation
set title = $
echo Enter your suffix
set suffix = $
set name = ($title $name $suffix )
echo Hello ${name}
@ i = $#name
set name = ( $name [1 -2] $name [4-$i] )
echo Hello ${name}
~/Tutorials/BASH/scripts/day1/examples ./name.sh
Print your first and last name
Alex Pacheco
Hello Alex Pacheco
Enter your salutation
Dr.
Enter your suffix
the first
Hello Dr. Alex Pacheco the first
Hello Dr. Alex the first
~/Tutorials/BASH/scripts/day1/examples ./name.csh
Print your first name
Alex
Print your last name
Pacheco
Hello Alex Pacheco
Enter your salutation
Dr.
Enter your suffix
the first
Hello Dr. Alex Pacheco the first
Hello Dr. Alex the first
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Command Line Arguments
Similar to programming languages, bash (and other shell scripting languages) can also
take command line arguments
./scriptname arg1 arg2 arg3 arg4 ...
$0,$1,$2,$3, etc: positional parameters corresponding to
./scriptname,arg1,arg2,arg3,arg4,... respectively
$#: number of command line arguments
$*: all of the positional parameters, seen as a single word
$@: same as $* but each parameter is a quoted string.
shift N: shift positional parameters from N+1 to $# are renamed to variable
names from $1 to $# - N + 1
In csh,tcsh
an array argv contains the list of arguments with argv[0] set to name of script.
#argv is the number of arguments i.e. length of argv array.
46 / 76

shift.sh
#!/bin/bash
USAGE=USAGE: $0 at least 1 argument
if [[ $# -lt 1 ]]; then
echo $USAGE
exit
fi
echo Number of Arguments: $#
echo List of Arguments: $@
echo Name of script that you are running: $0
echo Command You Entered: $0 $*
while [ $# -gt 0 ]; do
echo Argument List is: $@
shift
done
shift.csh
#!/bin/tcsh
set USAGE=USAGE: $0 at least 1 argument
if ( $#argv 1 ) then
echo $USAGE
exit
endif
echo Number of Arguments: $#argv
echo List of Arguments: ${argv}
echo Command You Entered: $0 ${argv}
while ( $#argv 0 )
echo Argument List is: $*
echo Number of Arguments: $#argv
shift
end
dyn100085:examples apacheco$ ./shift.sh $(seq 1 5)
Number of Arguments: 5
List of Arguments: 1 2 3 4 5
Name of script that you are running: ./shift.sh
Command You Entered: ./shift.sh 1 2 3 4 5
Argument List is: 1 2 3 4 5
Argument List is: 2 3 4 5
Argument List is: 3 4 5
Argument List is: 4 5
Argument List is: 5
dyn100085:examples apacheco$ ./shift.csh $(seq 1 5)
List of Arguments: 1 2 3 4 5
Name of script that you are running: ./shift.csh
Command You Entered: ./shift.csh 1 2 3 4 5
Argument List is: 1 2 3 4 5
Argument List is: 2 3 4 5
Argument List is: 5
47 / 76

Declare command
Use the declare command to set variable and functions attributes.
Create a constant variable i.e. read only variable
Syntax:
declare -r var
declare -r varName=value
Create an integer variable
Syntax:
declare -i var
declare -i varName=value
You can carry out arithmetic operations on variables declared as integers
~/Tutorials/BASH j=10/5 ; echo $j
10/5
~/Tutorials/BASH declare -i j; j=10/5 ; echo $j
2
48 / 76

Functions I
Like ”real” programming languages, bash has functions.
A function is a subroutine, a code block that implements a set of operations, a ”black
box” that performs a specified task.
Wherever there is repetitive code, when a task repeats with only slight variations in
procedure, then consider using a function.
function function_name {
command
}
OR
function_name () {
command
}
49 / 76

Functions II
shift10.sh
#!/bin/bash
usage () {
echo USAGE: $0 [atleast 11 arguments]
exit
}
[[ $# -lt 11 ]] usage
echo List of Arguments: $@
echo Command You Entered: $0 $*
echo First Argument $1
echo Tenth and Eleventh argument $10 $11 ${10}
${11}
shift 9
dyn100085:examples apacheco$ ./shift10.sh
USAGE: ./shift10.sh [atleast 11 arguments]
dyn100085:examples apacheco$ ./shift10.sh $(seq 1 10)
USAGE: ./shift10.sh [atleast 11 arguments]
dyn100085:examples apacheco$ ./shift10.sh ‘seq 1 2 22‘
List of Arguments: 1 3 5 7 9 11 13 15 17 19 21
Name of script that you are running: ./shift10.sh
Command You Entered: ./shift10.sh 1 3 5 7 9 11 13 15 17 19
21
First Argument 1
Tenth and Eleventh argument 10 11 19 21
Argument List is: 1 3 5 7 9 11 13 15 17 19 21
dyn100085:examples apacheco$ ./shift10.sh $(seq 21 2 44)
List of Arguments: 21 23 25 27 29 31 33 35 37 39 41 43
Name of script that you are running: ./shift10.sh
Command You Entered: ./shift10.sh 21 23 25 27 29 31 33 35
37 39 41 43
First Argument 21
Tenth and Eleventh argument 210 211 39 41
Argument List is: 21 23 25 27 29 31 33 35 37 39 41 43
50 / 76

Functions III
You can also pass arguments to a function.
All function parameters or arguments can be accessed via $1, $2, $3,..., $N.
$0 always point to the shell script name.
$* or $@ holds all parameters or arguments passed to the function.
$# holds the number of positional parameters passed to the function.
Array variable called FUNCNAME contains the names of all shell functions currently in
the execution call stack.
By default all variables are global.
Modifying a variable in a function changes it in the whole script.
You can create a local variables using the local command
Syntax:
local var=value
local varName
51 / 76

Functions IV
A function may recursively call itself even without use of local variables.
factorial3.sh
#!/bin/bash
usage () {
echo USAGE: $0 integer
exit
}
factorial () {
local i=$1
local f
declare -i i
declare -i f
if [[ $i -le 2 $i -ne 0 ]]; then
echo $i
elif [[ $i -eq 0 ]]; then
echo 1
else
f=$(( $i - 1 ))
f=$( factorial $f )
f=$(( $f * $i ))
echo $f
fi
}
if [[ $# -eq 0 ]]; then
usage
else
for i in $@ ; do
x=$( factorial $i )
echo Factorial of $i is $x
done
fi
dyn100085:examples apacheco$ ./factorial3.sh $(seq 1 2 11)
Factorial of 1 is 1
Factorial of 3 is 6
Factorial of 5 is 120
52 / 76

Scripting for Job Submission
Problem Description
I have to run more than one serial job.
Solution: Create a script that will submit and run multiple serial jobs.
I don’t want to submit multiple jobs using the serial queue since
Cluster Admins give lower priority to jobs that are not parallelized
The number of jobs that I want to run exceed the maximum number of jobs that
I can run simultaneously
How do I submit one job which can run multiple serial jobs?
One Solution of many
Write a script which will log into all unique nodes and run your serial jobs in
background.
Easy said than done
What do you need to know?
1 Shell Scripting
2 How to run a job in background
3 Know what the wait command does
53 / 76

[alp514.sol ](1012): cat checknodes.slr
#!/bin/bash
#
#SBATCH --partition=lts
#SBATCH --ntasks -per -node =4
#SBATCH --nodes =4
#SBATCH --time =5
#SBATCH --output=nodetest.out
#SBATCH --error=nodetest.err
#SBATCH --job -name=testing
#
export WORK_DIR=${ SLURM_SUBMIT_DIR }
srun -s hostname hostfile
export NPROCS=‘wc -l hostfile |gawk ’//{ print $1}’‘
NODES =(‘cat hostfile ‘ )
UNODES =(‘sort hostfile | uniq ‘ )
echo ‘‘Nodes Available: ‘‘ ${NODES[@]}
echo ‘‘Unique Nodes Available: ‘‘ ${UNODES[@]}
echo ‘‘Get Hostnames for all processes ’’
i=0
for nodes in ‘‘${NODES[@]}’’; do
ssh -n $nodes ’echo $HOSTNAME ’$i ’ ’
let i=i+1
done
wait
echo ‘‘Get Hostnames for all unique nodes ’’
i=0
NPROCS=‘sort hostfile | uniq | wc -l |gawk ’//{ print $1}’‘
let NPROCS -=1
while [ $i -le $NPROCS ] ; do
ssh -n ${UNODES[$i]} ’echo $HOSTNAME ’$i ’ ’
let i=i+1
done
[alp514.sol ](1013): sbatch -p imlab checknodes.slr
Submitted batch job 620045
54 / 76

[alp514.sol ](1014): cat nodetest.out
Nodes Available: sol -b411 sol -b411 sol -b411 sol -b411 sol -b413 sol -b412 sol -b501 sol -b413 sol -b413 sol -b413
sol -b412 sol -b412 sol -b412 sol -b501 sol -b501 sol -b501
Unique Nodes Available: sol -b411 sol -b412 sol -b413 sol -b501
Get Hostnames for all processes
sol -b501 14
sol -b501 6
sol -b501 15
sol -b501 13
sol -b413 4
sol -b413 9
sol -b412 11
sol -b412 10
sol -b413 7
sol -b413 8
sol -b412 5
sol -b411 1
sol -b412 12
sol -b411 3
sol -b411 2
sol -b411 0
Get Hostnames for all unique nodes
sol -b411 0
sol -b412 1
sol -b413 2
sol -b501 3
55 / 76

grep
grep is a Unix utility that searches through either information piped to it or files in the
current directory.
egrep is extended grep, same as grep -E
Use zgrep for compressed files.
Usage: grep options search pattern files
Commonly used options
Option Operation
-i ignore case during search
-r search recursively
-v invert match i.e. match everything except pattern
-l list files that match pattern
-L list files that do not match pattern
-n prefix each line of output with the line number within its input file.
-A num print num lines of trailing context after matching lines.
-B num print num lines of leading context before matching lines.
57 / 76

sed
sed (“stream editor”) is Unix utility for parsing and transforming text files.
sed is line-oriented, it operates one line at a time and allows regular expression
matching and substitution.
sed has several commands, the most commonly used command and sometime the only
one learned is the substituion command, s
~/Tutorials/BASH/scripts/day1/examples cat hello.sh | sed ’s/bash/tcsh/g’
#!/bin/tcsh
# My First Script
echo ‘‘Hello World!’’
List of sed pattern flags and commands line options
Pattern Operation
s substitution
g global replacement
p print
I ignore case
d delete
G add newline
w write to file
x exchange pattern with hold buffer
h copy pattern to hold buffer
Command Operation
-e combine multiple commands
-f read commands from file
-h print help info
-n disable print
-V print version info
-i in file subsitution
sed one-liners: http://sed.sourceforge.net/sed1line.txt
sed is a handy utility very useful for writing scripts for file manipulation.
58 / 76

The Awk text-processing language is useful for such tasks as:
F Tallying information from text files and creating reports from the results.
F Adding additional functions to text editors like “vi”.
F Translating files from one format to another.
F Creating small databases.
F Performing mathematical operations on files of numeric data.
Awk has two faces:
F it is a utility for performing simple text-processing tasks, and
F it is a programming language for performing complex text-processing tasks.
awk comes in three variations
awk : Original AWK by A. Aho, B. W. Kernighnan and P. Weinberger
nawk : New AWK, ATT’s version of AWK
gawk : GNU AWK, all linux distributions come with gawk. In some distros, awk is a
symbolic link to gawk.
Simplest form of using awk
awk pattern {action}
Most common action: print
Print file dosum.sh: awk ’{print $0}’ dosum.sh
Print line matching bash in all files in current directory:
awk ’/bash/{print $0}’ *.sh
60 / 76

awk patterns may be one of the following
BEGIN : special pattern which is not tested against input.
Mostly used for preprocessing, setting constants, etc. before input is read.
END : special pattern which is not tested against input.
Mostly used for postprocessing after input has been read.
/regular expression/ : the associated regular expression is matched to each input line that
is read
relational expression : used with the if, while relational operators
: logical AND operator used as pattern1 pattern2.
Execute action if pattern1 and pattern2 are true
|| : logical OR operator used as pattern1 —— pattern2.
Execute action if either pattern1 or pattern2 is true
! : logical NOT operator used as !pattern.
Execute action if pattern is not matched
?: : Used as pattern1 ? pattern2 : pattern3.
If pattern1 is true use pattern2 for testing else use pattern3
pattern1, pattern2 : Range pattern, match all records starting with record that matches
pattern1 continuing until a record has been reached that matches pattern2
print expression is the most common action in the awk statement. If formatted output
is required, use the printf format, expression action.
Format specifiers are similar to the C-programming language
%d,%i : decimal number
%e,%E : floating point number of the form [-]d.dddddd.e[±]dd. The %E format
uses E instead of e.
%f : floating point number of the form [-]ddd.dddddd
61 / 76

%g,%G : Use %e or %f conversion with nonsignificant zeros truncated. The %G
format uses %E instead of %e
%s : character string
Format specifiers have additional parameter which may lie between the % and the
control letter
0 : A leading 0 (zero) acts as a flag, that indicates output should be padded
with zeroes instead of spaces.
width : The field should be padded to this width. The field is normally padded
with spaces. If the 0 flag has been used, it is padded with zeroes.
.prec : A number that specifies the precision to use when printing.
string constants supported by awk
: Literal backslash
n : newline
r : carriage-return
t : horizontal tab
v : vertical tab
~/Tutorials/BASH/scripts/day1/examples echo hello 0.2485 5 | awk ’{printf ‘‘%s t %f n %d v %0.5d
n’’,$1 ,$2 ,$3 ,$3}’
hello 0.248500
5
00005
The print command puts an explicit newline character at the end while the printf
command does not.
62 / 76

awk has in-built support for arithmetic operations
Operation Operator
Addition +
Subtraction -
Multiplication *
Division /
Exponentiation **
Modulo %
Assignment Operation Operator
Autoincrement ++
Autodecrement –
Add result to varibale +=
Subtract result from variable -=
Multiple variable by result *=
Divide variable by result /=
~/Tutorials/BASH/scripts/day1/examples echo | awk ’{print 10%3} ’
1
~/Tutorials/BASH/scripts/day1/examples echo | awk ’{a=10; print a/=5}’
2
awk also supports trignometric functions such as sin(expr) and cos(expr) where expr is
in radians and atan2(y/x) where y/x is in radians
~/Tutorials/BASH/scripts/day1/examples echo | awk ’{pi=atan2 (1 ,1) *4; print pi ,sin(pi),cos(pi)}’
3.14159 1.22465e -16 -1
63 / 76

Other Arithmetic operations supported are
exp(expr) : The exponential function
int(expr) : Truncates to an integer
log(expr) : The natural Logarithm function
sqrt(expr) : The square root function
rand() : Returns a random number N between 0 and 1 such that 0 ≤ N 1
srand(expr) : Uses expr as a new seed for random number generator. If expr is not
provided, time of day is used.
awk supports the if and while conditional and for loops
if and while conditionals work similar to that in C-programming
if ( condition ) {
command1 ;
command2
}
while ( condition ) {
command1 ;
command2
}
64 / 76

awk supports if ... else if .. else conditionals.
if (condition1) {
command1 ;
command2
} else if (condition2 ) {
command3
} else {
command4
}
Relational operators supported by if and while
== : Is equal to
!= : Is not equal to
: Is greater than
= : Is greater than or equal to
: Is less than
= : Is less than or equal to
∼ : String Matches to
!∼ : Doesn’t Match
~/Tutorials/BASH/scripts/day1/examples awk ’{if (NR 0 ){print NR ,’’:’’, $0}}’ hello.sh
1 : #!/bin/bash
2 :
3 : # My First Script
4 :
5 : echo ‘‘Hello World!’’
65 / 76

The for command can be used for processing the various columns of each line
~/Tutorials/BASH/scripts/day1/examples echo $(seq 1 10) | awk ’BEGIN{a=6}{ for (i=1;i=NF;i++){a+=$i
}}END{print a}’
61
Like all progamming languages, awk supports the use of variables. Like Shell, variable
types do not have to be defined.
awk variables can be user defined or could be one of the columns of the file being
processed.
~/Tutorials/BASH/scripts/day1/examples awk ’{print $1}’ hello.sh
#!/bin/bash
#
echo
~/Tutorials/BASH/scripts/day1/examples awk ’{col=$1;print col ,$2}’ hello.sh
#!/bin/bash
# My
echo ‘‘Hello
Unlike Shell, awk variables are referenced as is i.e. no $ prepended to variable name.
awk one-liners: http://www.pement.org/awk/awk1line.txt
66 / 76

awk can also be used as a programming language.
The first line in awk scripts is the shebang line (#!) which indicates the location of the awk
binary. Use which awk to find the exact location
On my Linux desktop, the location is /usr/bin/awk.
If unsure, just use /usr/bin/env awk
hello.awk
#!/usr/bin/awk -f
BEGIN {
print Hello World!
}
~/Tutorials/BASH/scripts/day2/examples ./hello.awk
Hello World!
To support scripting, awk has several built-in variables, which can also be used in one line
commands
ARGC : number of command line arguments
ARGV : array of command line arguments
FILENAME : name of current input file
FS : field separator
OFS : output field separator
ORS : output record separator, default is newline
67 / 76

awk permits the use of arrays
arrays are subscripted with an expression between square brackets ([· · · ])
hello1.awk
#!/usr/bin/awk -f
BEGIN {
x[1] = Hello ,
x[2] = World!
x[3] = n
for (i=1;i =3;i++)
printf %s, x[i]
}
~/Tutorials/BASH/scripts/day2/examples ./hello1.awk
Hello , World!
Use the delete command to delete an array element
awk has in-built functions to aid writing of scripts
length : length() function calculates the length of a string.
toupper : toupper() converts string to uppercase (GNU awk only)
tolower : tolower() converts to lower case (GNU awk only)
split : used to split a string. Takes three arguments: the string, an array and a
separator
gsub : add primitive sed like functionality. Usage gsub(/pattern/,”replacement
pattern”,string)
68 / 76

getline : force reading of new line
Similar to bash, GNU awk also supports user defined function
#!/usr/bin/gawk -f
{
if (NF != 4) {
error(‘‘Expected 4 fields ’’);
} else {
print;
}
}
function error ( message ) {
if (FILENAME != ‘‘-’’) {
printf (‘‘%s: ‘‘, FILENAME) ‘‘/dev/tty ’’;
}
printf(‘‘line # %d, %s, line: %sn’’, NR , message , $0)
‘‘/dev/tty ’’;
}
69 / 76

getcpmdvels.sh
#!/bin/bash
narg =($#)
if [ $narg -ne 2 ]; then
echo 2 arguments needed :[ Number of atoms] [Velocity file ]n
exit 1
fi
natom=$1
vels=$2
cat TRAJECTORY |
awk ’{ if ( NR % ’$natom ’ == 0){
printf %s %s %sn,$5 ,$6 ,$7
}else{
printf %s %s %s,$5 ,$6 ,$7
}
}’ $vels
getengcons.sh
#!/bin/bash
bash bash
GMSOUT=$1
grep ’TIME MODE ’ $GMSOUT | head -1 energy.dat
awk ’/ FS BOHR /{ getline;print }’ $GMSOUT energy.dat
70 / 76

#!/bin/bash
narg =($#)
if [ $narg -ne 6 ]; then
echo 4 arguments needed: [GAMESS output file] [Number of atoms] [Time Step (fs)] [ Coordinates file] [
Velocity file] [Fourier Transform Vel. File]
exit 1
fi
gmsout=$1
natoms=$2
deltat=$3
coords=$4
vels=$5
ftvels=$6
au2ang =0.5291771
sec2fs =1e15
mass=mass.dat
rm -rf $vels $coords $ftvels
######## Atomic Masses (needed for MW Velocities) ##########
cat $gmsout | sed -n ’/ATOMIC ISOTOPES /,/1 ELECTRON/p’ |
egrep -i = |
sed -e ’s/=//g’ |
xargs | awk ’{for (i=2;i=NF;i+=2){printf %sn,$i;printf %sn,$i;printf %sn,$i}}’ $mass
## Use the following with grep ####
#grep -i -A1 ’ATOMIC ISOTOPES ’ $gmsout |
# grep -iv atomic |
# awk ’{for (i=2;i=NF;i+=2){printf %sn,$i;printf %sn,$i;printf %sn,$i}}’ $mass
## Use the following with grep and sed ####
#grep -i -A1 ’ATOMIC ISOTOPES ’ $gmsout |
# sed -e ’/ATOMIC/d’ -e ’s/[0 -9]=//g’ |
# awk ’{for (i=1;i=NF;i+=1){printf %sn,$i;printf %sn,$i;printf %sn,$i}}’ $mass
######## Coordinates and Velocities ########################
awk ’/ CARTESIAN COORDINATES / {
icount =3;
printf %dnn,’$natoms ’
while (getline 0 icount =7){
print $0 ;
++ icount
}
}’ $gmsout | sed ’/----/d’ tmp.$$
#egrep -i -A5 ’cartesian coordinates ’ $gmsout |
71 / 76

# sed -e ’/CARTESIAN/d’ -e ’/----/d’ tmp.$$
#
cat tmp.$$ | cut -c -42 |
awk ’{if ( NF == 4){
printf %4.2f %9.6f %9.6f %9.6fn,$1 ,$2*’$au2ang ’,$3*’$au2ang ’,$4*’$au2ang ’
} else {
print $0
}
}’ $coords
cat tmp.$$ | cut -c 42- | sed ’/^ *$/d’ |
awk ’{if ( NR % ’$natoms ’ ==0){
printf %15.8e %15.8e %15.8en,$1*’$sec2fs ’,$2*’$sec2fs ’,$3*’$sec2fs ’
}
else {
printf %15.8e %15.8e %15.8e,$1*’$sec2fs ’,$2*’$sec2fs ’,$3*’$sec2fs ’
}
}’ $vels
rm -rf tmp.$$
octave -q EOF
vels=load($vels);
atmass=load($mass);
atmass=diag(atmass);
mwvels=vels*atmass;
ftmwvels=abs(fft(mwvels));
N=rows(ftmwvels);
M=columns(ftmwvels);
deltaw =1/N/$deltat;
fid=fopen($ftvels,w);
for I=[1:N]
sumft =0;
for J=[1:M]
sumft=sumft+ftmwvels(I,J)^2;
endfor
fprintf(fid , %15.8e %21.14en ,(I-1)*deltaw ,sumft);
endfor
fclose(fid);
EOF
72 / 76

getmwvels.awk
#!/usr/bin/awk -f
BEGIN{
if(ARGC 3){
printf 3 arguments needed :[ Gaussian log file] [Number of atoms] [MW Velocity file ]n;
exit;
}
gaulog = ARGV [1];
natom = ARGV [2];
vels = ARGV [3];
delete ARGV [2];
delete ARGV [3];
}
/^ *MW Cartesian velocity :/ {
icount =1;
while (( getline 0) icount = natom +1){
if(icount =2){
gsub (/D/,E) ;
printf %16.8e%16.8e%16.8e,$4 ,$6 ,$8 vels;
}
++ icount;
}
printf n vels;
}
73 / 76

gettrajxyz.awk
#!/usr/bin/awk -f
BEGIN{
if(ARGC 3){
printf 3 arguments needed :[ Gaussian log file] [Number of atoms] [Coordinates file ]n;
exit;
}
gaulog = ARGV [1];
natom = ARGV [2];
coords = ARGV [3];
delete ARGV [2];
delete ARGV [3];
}
/^ *Input orientation :/ {
icount =1;
printf %dnn,natom coords;
while (( getline 0)icount = natom +4){
if(icount =5){
printf %5d%16.8f%16.8f%16.8fn,$2 ,$4 ,$5 ,$6 coords;
}
++ icount;
}
}
74 / 76

References Further Reading
BASH Programming http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html
Advanced Bash-Scripting Guide http://tldp.org/LDP/abs/html/
Regular Expressions http://www.grymoire.com/Unix/Regular.html
AWK Programming http://www.grymoire.com/Unix/Awk.html
awk one-liners: http://www.pement.org/awk/awk1line.txt
sed http://www.grymoire.com/Unix/Sed.html
sed one-liners: http://sed.sourceforge.net/sed1line.txt
CSH Programming http://www.grymoire.com/Unix/Csh.html
csh Programming Considered Harmful
http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
Wiki Books http://en.wikibooks.org/wiki/Subject:Computing
76 / 76

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