Removal of extra spaces in *.log files to allow extraction of frequencies
Our university has upgraded its version of a computational chemistry program that our group uses quite regularly. In the past we have been able to extract frequency spectra from log files that are generated. Since the upgrade, the viewing program errors out. I've been able to trace down the changes between the old and new log file formats. The new program adds two extra spaces to the following lines:
Code:
Atom AN X Y Z X Y Z X Y Z
1 30 0.00 0.00 0.03 0.09 -0.02 0.04 0.10 -0.01 -0.03
2 8 0.03 -0.01 -0.12 -0.14 -0.08 -0.06 -0.14 -0.05 0.06
One space before Atom and one of the spaces between AN and Atom needs removed as there are two and should be only one space prior to each. On the next line there are five spaces and there should only be three before the atom number or the number starting the second and each successive line. The log file has each frequency broken up into columns of three frequencies so depending on how complex the molecular system is, this can become an impossible job to complete on thousands of files. Once the format is corrected, then everything opens fine and the frequencies can be extracted. The software developer is aware of this issue but advises the generation of a special portable file that would normally be used to transport data across platforms. The above data does have its tabs removed between each column as when I copied and pasted the contents, its formatting was removed. There are multiple instances of the above lines that then have a varied number of atoms listed below each column of three and the entire data set ends with a blank line where the thermochemistry data starts. Since these job files are processed via a bash script to extra thermodynamics and electronic energies, I thought it would be fairly simple to incorporate any new commands into the torque execution script. Any help would be greatly appreciated.
Last edited by Scrutinizer; 04-22-2013 at 01:22 AM..
Reason: code tags
Hi...
I am quite new to Unix and would like an issue to be resolved.
I have a file in the format below;
4,Reclaim,ECXTEST02,abc123,Harry Potter,5432 6730 0327 5469,0603,,MC,,1200,EUR,sho-001,,1,,,abc123,1223
I would like my output to be as follows;
4,Reclaim,ECXTEST02,abc123,Harry... (4 Replies)
Hi,
I have a string like this and i want to remove extra spaces that exists between the words.
Here is the sentence.
$string="The small DNA genome of hepadnaviruses is replicated by reverse transcription via an RNA intermediate. This RNA "pregenome" contains ... (2 Replies)
Hi,
I'm a newbie to shell scripting and I have the following problem:
I need all spaces between two letters or a letter and a number exchanged for an underscore, but all spaces between a letter and other characters need to remain. Searching forums didn't help...
One example for clarity:
... (3 Replies)
Hello..
I have a text file. I want to remove all the blank spaces(except tab) from the file..
I tried using sed command as shown below
sed 's/ //g' file1
But the problem with the above command is that it also eliminates 'tab' which is between the columns..
For example if the contents... (7 Replies)
Hi everyone..
I'm trying to eliminate multiple whitespaces from a file..
I must make use of shell script to eliminate whitespaces..
Take a look at the sample file
1 int main()
2 {
3 int a,b;
4 printf("Enter the values of a and b");
5 scanf("%d%d",&a,&b);
6 if(a>b) ... (6 Replies)
Hi I'm trying to remove blank spaces in expressions and function calls..
Consider the following example
printf ("Hello");
a = a + b;
I'm trying to eliminate space in between the function name and the opening brace. And also eliminate space between operators and operands..
That is, I'm... (19 Replies)
HI,
I need the help from the experts like I have created one file with text like:
a b c d
e f g h
i j k l
So my question is that i have to write the script in which like in the first sentence it will take only one space after d and remove all the extra space in the end.I dont... (8 Replies)
Hello All,
I have developed a script which takes following parameter from the input file to archive log files
1)Input Path
2)File pattern(*.csv)
3)Number of days(+1)
Following is the algorithm of my script
Read the input file
go to that path and search for particular n days older... (3 Replies)
hi,
i need to remove the extra spaces in the filed.
Sample:
abc~bd ~bkd123 .. 1space
abc~badf ~bakdsf123 .. 2space
abc~bqed ~bakuowe .. 3space
output:
abc~bd ~bkd123 .. 1space
abc~badf~bakdsf123 .. 2space
abc~bqed~bakuowe .. 3space
i used the following command, (2 Replies)
Hello,
I have an xml file and my aim is to grab each line in keywords file and search the string in another file.
When keyword is found in xml file,I expect the script to go to previous line in the xml file and grab the string/value between two strings. It's almost working with an error.
tab... (6 Replies)
Discussion started by: baris35
6 Replies
LEARN ABOUT ULTRIX
ppmtosixel
ppmtosixel(1) General Commands Manual ppmtosixel(1)NAME
ppmtosixel - convert a portable pixmap into DEC sixel format
SYNOPSIS
ppmtosixel [-raw] [-margin] [ppmfile]
DESCRIPTION
Reads a portable pixmap as input. Produces sixel commands (SIX) as output. The output is formatted for color printing, e.g. for a DEC
LJ250 color inkjet printer.
If RGB values from the PPM file do not have maxval=100, the RGB values are rescaled. A printer control header and a color assignment table
begin the SIX file. Image data is written in a compressed format by default. A printer control footer ends the image file.
OPTIONS -raw If specified, each pixel will be explicitly described in the image file. If -raw is not specified, output will default to com-
pressed format in which identical adjacent pixels are replaced by "repeat pixel" commands. A raw file is often an order of magni-
tude larger than a compressed file and prints much slower.
-margin
If -margin is not specified, the image will be start at the left margin (of the window, paper, or whatever). If -margin is speci-
fied, a 1.5 inch left margin will offset the image.
PRINTING
Generally, sixel files must reach the printer unfiltered. Use the lpr -x option or cat filename > /dev/tty0?.
BUGS
Upon rescaling, truncation of the least significant bits of RGB values may result in poor color conversion. If the original PPM maxval was
greater than 100, rescaling also reduces the image depth. While the actual RGB values from the ppm file are more or less retained, the
color palette of the LJ250 may not match the colors on your screen. This seems to be a printer limitation.
SEE ALSO ppm(5)AUTHOR
Copyright (C) 1991 by Rick Vinci.
26 April 1991 ppmtosixel(1)