lammps | Public development project of the LAMMPS MD software package

What's means of *=*gpu in conda/pip install?

See below:

I want to slice the following text

I am a newbie at programming and molecular dynamic simulations. I am using LAMMPS to simulate a physical vapor deposition (PVD) process and to determine the interactions between atoms in different timesteps.

After I perform a molecular dynamics simulation, LAMMPS provides me an output bonds file that contains records of every individual atom( as atom ID), their types (numbers reciprocating to particular elements), and information of other atoms that are bonded with those particular atoms. A typical bonds file looks like this.

I aim to sort atoms according to their types (like Group1: Oxygen-Hydrogen-Hydrogen) in three groups by considering their bonding information from bond output file and count the number of groups for each timestep. I used pandas and created a dataframe for each timestep.

I am not very familiar with bash programming. And I tried to write a bash script to reduce my work. what I want is to open the in.lammps file in every folder in this directory and replace some string in the in.lammps file. but it shows such an error. and I also did try:

I am trying to untar a file (new to Bash on Ubuntu on Windows), but it's showing an error. I have saved the file on the proper directory.

drsonamani@LAPTOP-23SII9GR:/$ tar xvzf lammps-stable.tar.gz tar (child): lammps-stable.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now

Any help

I have a a big text file which content something of the following:

First, I would like to apologize for my extremely basic knowledge about coding. Then I hope that I will be able to express myself correctly about my issue. Do no hesitate to ask for further clarifications or anything else...

I'm encountering troubles postprocessing data...

My goal is to recombine data which were swapped.

EDIT : here is a .rar folder containing my test example which works and the one that I try to make working... (do not be afraid by the time it requires to process the data)

https://drive.google.com/file/d/1AEPUc8haT5_Z3LR3jnZZlpyfxhdDwwo6/view?usp=sharing

EDIT 2 : Here is what I expect on paper (Its my TestReorder3OK folder in my rar archive)

enter image description here

EDIT 3 : MINIMAL COMPLETE EXAMPLE

Script :

I tried to install lammps on my department machine with a newer version of 11Aug17. However, mpicxx gives error to the following lines:

I have data for N atoms including the radius of each atom, the position of each atom and the box dimensions. I want to calculate the number of atoms each atom is in contact with and store the result. This is equivalent to calculating the number of atoms within a specified cutoff distance.

The box has periodic boundary conditions, and hence a difficulty arises in remapping atoms such that the distance calculated between each atom is the minimum possible.

Here is what I have so far: