How can I load my output data from output file 4.pair.p into a lammps.tjr file?

LAMMPS LAMMPS Beginners
,
1

If I run 1000000 steps, then

  1. visualize your trajectories every 10000 steps, plot 100 snapshots in the time sequence.
  2. plot temperatures. Pressure energy volume, as function of simulation steps. x-axis is 1000000steps, y-axis is your temperatures, pressure, energy, volume.
    I got two data data sets of information in my output file which are as follow;
    (a) per atom data
    ****** 256 particles

    type position el. den. energy

1   1     -8.1184   -8.1184   10.8246   0.000       -0.07255
2   1     -8.1184   -8.1184    5.4123   0.000       -0.07255
3   1     -5.4123   -8.1184    8.1184   0.000       -0.07255
4   1     -2.7061   -8.1184   10.8246   0.000       -0.07255
5   1     -8.1184   -5.4123    8.1184   0.000       -0.07255
6   1     -5.4123   -5.4123   10.8246   0.000       -0.07255
7   1     -8.1184   -2.7061   10.8246   0.000       -0.07255
8   1     -8.1184   -8.1184    0.0000   0.000       -0.07255
9   1     -5.4123   -8.1184    2.7061   0.000       -0.07255

10 1 -2.7061 -8.1184 5.4123 0.000 -0.07255

(b) volume, energy every 10,000 steps
output: 10000 -18.4439 -530.444 9869.05 256 0
output: 20000 -18.2303 -530.230 9815.59 256 0
output: 30000 -18.0670 -530.067 9724.29 256 0
output: 40000 -17.8795 -529.880 9895.16 256 0
output: 50000 -17.8162 -529.816 9794.11 256 0
output: 60000 -17.7131 -529.713 9821.34 256 0
output: 70000 -17.6202 -529.620 9989.19 256 0
output: 80000 -17.5797 -529.580 9907.50 256 0
output: 90000 -17.4802 -529.480 9856.73 256 0
output: 100000 -17.4759 -529.476 9936.82 256 0
output: 110000 -17.3940 -529.394 9977.86 256 0
output: 120000 -17.3027 -529.303 9985.06 256 0
output: 130000 -17.3214 -529.321 10065.4 256 0
output: 140000 -17.2887 -529.289 10019.1 256 0
output: 150000 -17.3180 -529.318 10065.9 256 0
output: 160000 -17.3423 -529.342 9986.31 256 0
output: 170000 -17.3675 -529.368 10046.4 256 0
output: 180000 -17.2456 -529.246 10094.8 256 0
output: 190000 -17.2706 -529.271 10106.8 256 0
output: 200000 -17.2627 -529.263 10117.8 256 0

2

Your question in the subject and the information provided are quite confusing and there is a lot of context missing.

To do the two tasks you mention, you do not need what you ask for in your subject.
Both tasks are straightforward to do and are not LAMMPS tasks but (standard) postprocessing tasks.

3

Actually I am confused about my output file which shows me two kind of data sets.
I have two different output files, which I described in details are as follow
1- 4.pair.p (printing information in two different data set)
(a) per atom data in row column structure showing the atom number from 1 to 256 with their type, there x y z coordinates, electron density, & energy. the output format looks like this,
****** 256 particles

type position el. den. energy

1   1     -8.1184   -8.1184   10.8246   0.000       -0.07255

.
.
.
256 1 10.8246 10.8246 -5.4123 0.000 -0.07255

(b) output every 10,000 steps like average energy, final energy, final volume, no of atoms. the format looks like this.
output: 10000 -18.4439 -530.444 9869.05 256 0
.
.
.
output: 1000000 -17.0573 -529.057 10121.3 256 0

(c) there are many other things which are shown in my output file 4.pair.p like jump types acceptance and rejection, total time for monte Carlo simulation, units explanations initial condition lattice generation information and periodic boundary conditions etc.

2- x.pair.r
The x.pair.r file is typically a restart file showing for average positions, it stores the current state of variables so that a simulation can be restarted from that point or the data can be analyzed or visualized later.
i) It shows a header like ‘ab alloy phase diagram’
ii) no of atom "256’ in my case
iii) periodic boundary condition
iv) atomic mass and element type
v) Average position & composition of each atom
The output in x.pair.r file looks like this;
ab Alloy Phase Diagram with LJ smoothcut potential
256 2
0.1111771146855224E+02 0.1056725489146267E+02 0.1073836518517207E+02
-0.1082458000000000E+02 -0.1082458000000000E+02 -0.1082458000000000E+02
0.4140610337373800E-02 18
0.4140610337373800E-02 18
-0.8254126517583805E+01 -0.7676814580573758E+01 -0.1065208990573025E+02
0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00
1
-0.8122654779154855E+01 -0.7958714904380413E+01 0.5134876439759154E+01
0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00
1

How can I achieve the goal of visualizing my trajectories every 10000 steps, plot 100 snapshots in the time sequence. How can I extract these data out and arrange them in the format of lammps.trj or .xyz format which can be recognized by OVITO.

4

Please study the documentation of the dump command.

I have no idea what you mean. Maybe thermo 100 is the command you want to use?

The bottom line is that if you are not able to explain what you want to achieve, then it is likely that you are not understanding what you are doing. Also, please read the forum rules, as your posts are visually a mess and conceptually hard to decipher.

5

Sorry I. understand the the inconvenience I created by my post.
And thankyou for your kind feedback