How to output the temperature of of beads in different time steps?

LAMMPS LAMMPS Beginners
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1

I am using edpd, energy conserved dissipative particle dynamics method to simulate a CNT inside water. For the output, I am getting the positions in space and the temperature and the density related to that position using the following commands:

compute temp all edpd/temp/atom

compute ccT all chunk/atom bin/3d x 0.0 100 y 0.0 100 z 0.0 100
fix stat all ave/chunk 1 6 1000 ccT c_temp density/number norm sample file
tempeditcnt.profile

My question is how can I output the temperature of each position as time passes (in different time steps). Sorry if this is a trivial question, but I could not find a method to output the temperature in timesteps to be used in edpd method (beads have internal temperature as well)

The first few commands of my code is:

units lj
dimension 3
boundary p p p
neigh_modify one 10000 delay 0 check yes

change neighbor list parameters to avoid dangerous builds

atom_style hybrid edpd full
bond_style harmonic
angle_style charmm

System definition

region edpd block -50 50 -50 30 -22 23 units box

read_data data.data

create_atoms 2 random 16000 276438 NULL

#grouping

group cnt type 1
group liquid type 2

mass 1 1
mass 2 12
set atom * edpd/temp 1.0
set atom * edpd/cv 1.0E5

pair_style edpd 1.58 9872598

bond_coeff 1 80.0 1.2
angle_coeff 1 300.0 107.0 50.0 3.0

pair_coeff * * 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 &
power 10.54 -3.66 3.44 -4.10 &
kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes

2

The easiest way to output per-atom quantities is through a dump file, the same way one would output the position (x, y, z) or velocity (vx, vy, vz). According to the atom_style page in the docs, atom_style edpd uses the quantity edpd_temp. Read the docs (Section 8.3.1 - Output from LAMMPS) for more info on outputting.

Sorry, re-reading your question, I don’t understand the issue. You’re already computing the average atomic temperature of each bin every 1000 timesteps, and they should be consecutively written to tempeditcnt.profile. What are the contents of the file after, say 5000 timesteps (perhaps for a smaller, test system)?

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3

Yes, I am getting the ave themperature of each bin, but I am looking for a way if possible to get the temperature of each bead. Is there anyway to output the the position and temperatute of each bead in every for example 100 timestep?

4

You can use a custom style dump.

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5

Thank you so much :slight_smile: