Themal Conductivity using Muller_plathe Aprroach

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1

Dear Lammps users

I am trying to kappa using in.mp script in lammps directory. But there is one variable defined

variable tdiff equal f_2[11][3]-f_2[1][3]

I want to know why we use [11][3] and [1][3] to calculate tdiff? What 11 and 3 refer to here?? Please clarify.

Thanks

Rajesh.

sample LAMMPS input script for thermal conductivity of liquid LJ

Muller-Plathe method via fix thermal_conductivity

settings

variable x equal 10
variable y equal 10
variable z equal 20

variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5

#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0

setup problem

units lj
atom_style atomic

lattice fcc ${rho}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0

velocity all create $t 87287

pair_style lj/cut ${rc}
pair_coeff 1 1 1.0 1.0

neighbor 0.3 bin
neigh_modify delay 0 every 1

1st equilibration run

fix 1 all nvt temp $t $t 0.5
thermo 100
run 1000

velocity all scale $t

unfix 1

2nd equilibration run

compute ke all ke/atom
variable temp atom c_ke/1.5

fix 1 all nve
fix 2 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
file profile.mp units reduced
fix 3 all thermal/conductivity 10 z 20

variable tdiff equal f_2[11][3]-f_2[1][3]
thermo_style custom step temp epair etotal f_3 v_tdiff

thermo 1000
run 20000

thermal conductivity calculation

reset fix thermal/conductivity to zero energy accumulation

fix 3 all thermal/conductivity 10 z 20

fix ave all ave/time 1 1 1000 v_tdiff ave running
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave

run 20000

2

Dear Lammps users

I am trying to kappa using in.mp script in lammps directory. But there is
one variable defined

variable tdiff equal f_2[11][3]-f_2[1][3]

I want to know why we use [11][3] and [1][3] to calculate tdiff? What 11 and
3 refer to here?? Please clarify.

please RTFM for a change.

axel.

3

Dear Axel

Thanks for your RTFM. Actually fix_2 is ave/spatial command which I could not find in the RTFM.

Thanks

Rajesh

4

Dear Axel

Thanks for your RTFM. Actually fix_2 is ave/spatial command which I could
not find in the RTFM.

then you are not using the right FM. your input is for an older
version of LAMMPS, so you'll have to use a correspondingly old manual
and in the OFM, you will find the description of fix ave/spatial.
BTW: at the beginning of any FM, it tells you to RTFM of the same
version of LAMMPS that you are using and that the online version
always corresponds to the latest patchlevel.

as you can see from http://lammps.sandia.gov/bug.html fix ave spatial
has been removed from the latest version in the may 31st 2016 patch.

axel.

5

The fix ave/spatial command is deprecated (if you
run your script in the current version of LAMMPS you
will see a message about this). The new command
is fix ave/chunk. In the current LAMMPS distro
that viscosity script uses fix ave/chunk.

PS: Let’s please not use RTFM on the public mail list.
“Read the manual” is sufficient advice.

Steve

6

Dear Steve

Thank you for your advice and sorry we did use the word.
Now, As I understand from manual, in
variable tdiff equal f_2[11][3]-f_2[1][3]

11 and 1 are for 11th and 1st bins respectively. Actually I want to compute average temperature of some groups of atoms. Can fix chunk/atom be used for the same? Please advise.

Thank you

Rajesh.

7

Dear Steve

Thank you for your advice and sorry we did use the word.
Now, As I understand from manual, in
variable tdiff equal f_2[11][3]-f_2[1][3]

11 and 1 are for 11th and 1st bins respectively. Actually I want to compute
average temperature of some groups of atoms. Can fix chunk/atom be used for
the same? Please advise.

just keep reading the fine manual:
http://lammps.sandia.gov/doc/fix_ave_chunk.html