[lammps-users] error on example of compute heat/flux

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1

Hi, I am trying a example give by the manual of command ‘computer heat flux’. While alway got an error ’ compute ID for fix ave/correlate does not exist’. I just updated Lammps and the version should not be the problem. Below is the script:

Sample LAMMPS input script

atom_style  atomic
units       real
variable    kB equal 1.3806504e-23 # **J/K** Boltzmann
variable    kCal2J equal 4186.0/6.02214e23
variable    T equal 70
variable    V equal vol
variable    dt equal 4.0
variable    p equal 200 # correlation length
variable    s equal 10  # sample interval
variable    d equal $p*$s # dump interval

---------------------------------------------------------

dimension    3
boundary     p p p
lattice      fcc  5.376  orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region       box block 0 4 0 4 0 4
create_box   1 box
create_atoms 1 box
mass	     1 39.948
pair_style   lj/cut 13.0
pair_coeff   * * 0.2381 3.405
timestep     $*dt*
thermo	     $d

------------- equilibration and thermalization ----------------

velocity  all create $T 102486 mom yes rot yes dist gaussian
fix       NVT all nvt temp $T $T 10 drag 0.2
run       8000

-------------- flux calculation ---------------

reset_timestep  0
compute   myKE all ke/atom
compute   myPE all pe/atom
compute   myStress all stress/atom virial
compute   flux all heat/flux myKE myPE myStress
variable  Jx equal c_flux**1**/vol
variable  Jy equal c_flux**2**/vol
variable  Jz equal c_flux**3**/vol
fix       JJ all ave/correlate $s $p $d &
          c_flux**1** c_flux**2** c_flux**3** type auto file J0Jt.dat ave running
variable  scale equal $*kCal2J**$*kCal2J*/$*kB*/$T/$T/$V*$s*$*dt**1.0e25
variable  k11 equal trap(f_JJ**3**)*$*scale*
variable  k22 equal trap(f_JJ**4**)*$*scale*
variable  k33 equal trap(f_JJ**5**)*$*scale*
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run       100000
variable  k equal (v_k11+v_k22+v_k33)/3.0
print     "average conductivity: $k **W/mK**"
2

It should be c_flux[1], not c_flux1.
It's just a formatting error
in the way the HTML for the doc page appears.
I just corrected it on the WWW site. Try looking
at the new page, there are several places that brackets
now appear in the commands.

Steve

3

Hi Steve, thanks for the modifications. While I got another error by using the new script:

“ERROR on proc 0: Substitution for illegal variable
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0”

4

ok - try cut/paste from the compute heat/flux doc page (on the
WWW site) one more time. This was again a formatting error
in the HTML with the curly braces around variables not passing
thru to the HTML.

Steve

2010/8/27 Tom Yu <[email protected]...>:

5

Thanks, it works now. While as I modified the second piece of the script to the following, i.e. I use my amorphous silica structure by ‘read data’, and use Tersoff potential, I was always given ‘Invalid pair style’. This position file and potential were already tested in other script, so these should not be the problem. I know the Tersoff potential file I used is only suitable for ‘metal’ unit, when I changed the unit in the sample script from ‘real’ to ‘metal’, I still got the same message. I am confused, even the potential parameters are wrong due to the mis-assigning of unit style, it should be nothing to do with the pair style.

---------------------------------------------------------

read_data sio
neighbor 0.3 bin
neigh_modify check yes
pair_style tersoff
pair_coeff * * sico.tersoff Si O
timestep ${dt}
thermo $d

6

Your system has 1 atom type (create box). The pair_coeff
command is trying to set up 2 atoms types - hence the error.

Steve

2010/9/2 Tom Yu <[email protected]...>:

7

I replaced the second part of sample script with my script shown in the last message, so I did not use ‘create box’ command but defined the box and the atoms positions in the configuration file. As shown below,

units real
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable T equal 70
variable V equal vol
variable dt equal 4.0
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval

---------------------------------------------------------

read_data sio
neighbor 0.3 bin
neigh_modify check yes
#pair_style tersoff
#pair_coeff * * sio.tersoff Si O
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep ${dt}
thermo $d

------------- equilibration and thermalization ----------------

…the following is the same with the sample

8

I don't know what your question is anymore.

Steve

2010/9/3 Tom Yu <[email protected]...>: