Dear Lammps users,
I have been performing Green-Kubo calculations of the thermal conductivity of various non-charged simple liquids using Lammps with great success.
I am now however trying to do the same for SPC/E water and am having trouble and was hoping someone might have experience with such a case.
The input script I am using is very similar to the example LJ system that is documented on the Lammps webpage, except with the appropriate SPC/E parameters/units and the starting configuration is read in via a read_restart command.
The thermalisation/equilibration “appears” to occur normally, however when the compute commands required for the Green-Kubo calculation are performed I get the error which is shown at the bottom of this email.
I attach a compressed directory containing the input script and restart file which I am using in case this is of any use. The origins of the restart file are that of a deformation run which I performed to achieve my desired volume.
Many thanks, Jeff.
Setting up run …
[ch-bresme-i7-4:19417] *** Process received signal ***
[ch-bresme-i7-4:19417] Signal: Segmentation fault (11)
[ch-bresme-i7-4:19417] Signal code: Address not mapped (1)
[ch-bresme-i7-4:19417] Failing at address: 0x5c6d2b8
spce_gk.tgz (1.08 KB)
dear jeff,
The thermalisation/equilibration "appears" to occur normally, however when
the compute commands required for the Green-Kubo calculation are performed I
get the error which is shown at the bottom of this email.
I attach a compressed directory containing the input script and restart file
which I am using in case this is of any use. The origins of the restart file
are that of a deformation run which I performed to achieve my desired
volume.
sorry, but LAMMPS restart files are not portable. so i cannot check your run.
if you want somebody to check things out, please convert it to a (portable)
data file and adjust your input script accordingly.
axel.
Thank you, here is an all in one scripted version of what I am doing. The script in broad terms does the following:
Read_data for the initial SPC/E configuration
Fix NVT and Deform for a box deformation
Short NVT thermalisation
short NVE relaxation
Green-Kubo NVE section
All run times have been set to very small values for testing purposes. The compressed data file and input script are attached.
Many thanks, Jeff.
spce_gk.tgz (123 KB)
thanks for the input.
the segmentation error has nothing to do
with thermal conductivity. it is a bug in the
recently updated pppm code that has been
fixed since. try the very latest lammps code
and it should work.
axel.