UT theoretical chemistry code forum

While the output from the Bader analysis in VNL may look similar to the bader program developed by Graeme's group, it is not the same program. The implementation in VNL uses the on-grid algorithm, which is not as accurate as the near-grid algorithm, which is used by default in the original bader ...

A question on Hyperdynamics: I added Hyperdynamics beneath my MD input and in the client.log file, I don't see any results on Hyperdynamics. It only shows DYNAMICS results. Please see the relevant input from config.ini file pasted below:


[Dynamics]
time_step = 1.0
time = 2000.0
thermostat ...

It might be as easy as changing LAMMPS_EON.cpp to set "atom_style charge". From the LAMMPS docs (http://lammps.sandia.gov/doc/atom_style.html) it looks like that shouldn't break anything. I made this change in the lastest SVN version but I have not tested it. You can try to update your svn copy and ...

Our L-BFGS implementation will never guarantee a monotonic decrease in energy. It does not use a "proper" line search. This is so that the same code can be easily used with NEB optimization, which does not have an energy function to optimize (instead the force on the images is optimized). The ...

I do not know when this script was written or what it is supposed to do or why it is named pos2exafs. It seems to compute the 1st NN radial distribution function, but that is just what it looks like at first glance. If you want to compute EXAFS you should use feff6-lite: http://www.feffproject.org ...

Could you please attach the full output of make? I'm not aware of any hdf5 dependence and the string "hdf5" doesn't appear in the code.

These patches are only needed for a special version of VASP designed to run with our long timescale dynamics package Eon. The patches will only apply cleanly to VASP 5.3.2. If you do not plan on running VASP with Eon then there is no need to apply the patches.

I think the reason you get that message is because NSW=0. This means VASP quits after the first calculation. That is why Eon complains about VASP dying. Could you try making NSW larger than the expected number of "steps" in your calculation? You can just set it to a huge number if you like.

I see what you mean. All that is need is to have the eon python module listed in the PYTHONPATH environment variable. If you have extracted eon to your home directory then the following line in your bash .profile file will install eon:

export PYTHONPATH=$HOME/eon:$PYTHONPATH

Or you can install the ...

Hi Liuxi,

The name of the exeuctable is "eonclient". The documentation was out of date so I have updated it.

I don't understand your other question. Could you rephrase it?

Thanks,
Sam

It looks like you have an old version of GCC that doesn't recognize the "-Wno-unused-local-typedefs" flag. This flag just tells GCC not to give a certain warning during compile. You can remove these type of flags by editing "eon/client/Makefile" and changing the line from:
CXXFLAGS += -Wall -Wno ...

There isn't any issue with using SCALAPACK and the VTSTCODE NEB as far as I am aware. Please report any issue you may find.

If the tsase directory is in "$HOME/code/tsase" then you need to add "$HOME/code" to your $PYTHONPATH. Does that help?

There hasn't been any performance difference in our compute client when compiled at -O3 as opposed to -O2.

This issue should be fixed. There was a bug in our work generation software that caused the delay. It should be working again!