how to read variables from a file and write to a new file?

taha95 has asked for the wisdom of the Perl Monks concerning the following question:
Hi, I have a data file (data.lammps, it has nearly 2000 lines or more) for water in carbon nanotube that connected to two reservoirs of water. this data file consist of atom number, molecule number, type of atom, charge of atoms and coordinates of atoms (x, y , z for carbon,hydrogen and oxygen) and bonds and angles for water molecules. I want to write a new file that read this data file and give me the coordinates of carbon nanotube and water moleculs in it (not reservoirs and water in them). In fact I want to read from a file and use some <for> and <if> clause to get a new data file. but i don't know how to define variables for reading a file(how define x , y, z ,.... in my data file).I'm a new user of perl and up to now I just write a perl script for writing to a file not reading. so I have som problems about this. please guide me. any code or example for doing this task is highly apperciated.
Many thanks in advance.
at the bottom there is three lines of my data file(data.lammps). I don't know how to upload my data file here.
LAMMPS data file via write_data, version 10 Feb 2015, timestep = 25000
+0

748 atoms
8 atom types
152 bonds
1 bond types
76 angles
1 angle types

-2.2135609320730300e+01 2.2135609320730300e+01 xlo xhi
-2.1300000000000001e+01 2.1300000000000001e+01 ylo yhi
-7.4410005469289999e+01 7.4410005469289999e+01 zlo zhi

Masses

1 1.008
2 12.01
3 12.01
4 12.01
5 12.01
6 12.01
7 12.01
8 16

Bond Coeffs # harmonic

1 0 0.9572

Angle Coeffs # harmonic

1 0 104.5

Atoms # full

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Comment on how to read variables from a file and write to a new file? Download Code
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Re: how to read variables from a file and write to a new file? by kcott (Archbishop) on May 30, 2017 at 08:41 UTC
G'day taha95, Welcome to the Monastery. This is very difficult to read. Whatever the original file format was is lost because it's all posted as plain text. In short, put all code and data within `<code>...</code>` tags. That way we can both see the format, and download a verbatin copy, for testing and analysing your problems. See "How do I post a question effectively?" for more about this. I'd first recommend reading "perlintro - Perl introduction for beginners". This will give you the basics of `for`, `if`, variables and I/O. Follow the links in each section, to more in-depth information, as required. — Ken	[reply] [d/l] [select]
Re: how to read variables from a file and write to a new file? by Anonymous Monk on May 30, 2017 at 08:35 UTC
Hi, Start with perlintro, open, readline, split ... get something started ... I don't know how to upload my data file here ... :) The details aren't hidden `Use: <p> text here (a paragraph) </p> and: <code> code here </code> to format your post; it's "PerlMonks-approved HTML":` [download] Atoms # full ?? LAMPPS / Large-scale Atomic/Molecular Massively Parallel Simulator ??	[reply] [d/l]
Re^2: how to read variables from a file and write to a new file? by taha95 (Initiate) on May 30, 2017 at 11:04 UTC
yes. i use lammps and need this data file for simulation in lammps.	[reply]
Re: how to read variables from a file and write to a new file? by pryrt (Abbot) on May 30, 2017 at 20:57 UTC
As a new user of Perl, you'll want to look up the documentation for each part of the task; the Anonymous Monk gave you links to some of the commands you'll need; each of those documents includes code snippets that show how to use them. If I were you, I would make a programming-language-agnostic outline of what needs to be done ("open input file, open output file, read input file one line at a time, for each line do something including writing to the output file"). Then delve into the documentation to try to figure it out what commands you need to perform those tasks. The perlintro that AM linked should help you with your question of how to get something into a variable. Once you've got example code, if it doesn't work, post a SSCCE which shows your code, a simple input file (smaller is better, as long as it's sufficient to show the problem), an example of what you'd like the output file to look like, and let us know what's going wrong and/or what errors you are seeing.	[reply]
Re: how to read variables from a file and write to a new file? by Marshall (Canon) on May 30, 2017 at 20:16 UTC
Hi taha95!, Your post of the input data file is now readable. I guess code tags were added? I don't and, probably very few here, understand the kind of output file that you want to generate. Can you give us an algorithm to do the processing? The folks here do know a lot about Perl, but probably very little if anything about "LAMMPS".	[reply]