Search found 39 matches

by xph
Fri Jul 26, 2019 10:30 pm
Forum: tsase
Topic: bugs in neb code
Replies: 2
Views: 1622

Re: bugs in neb code

I was worried in the beginning, but later found out that all the "vproj" calls are projecting forces on to a unit vector (tangent direction), except in dneb. So dneb was totally messed up, but the regular (ss)neb was good.
by xph
Thu May 12, 2016 8:47 pm
Forum: VTSTTools
Topic: Is G-SSNEB available now?
Replies: 29
Views: 19633

Re: Is G-SSNEB available now?

SSDimer is only available in our TSASE package, not in the VTSTCODE. TSASE can invoke VASP as calculator too, but I strongly recommend trying an empirical potential first because SSDimer searches are really expensive. See the page here for more details: http://theory.cm.utexas.edu/tsase/ssdimer.html...
by xph
Tue Nov 03, 2015 6:30 pm
Forum: eOn
Topic: EON -- how to deal with charges on the atom
Replies: 13
Views: 22472

Re: EON -- how to deal with charges on the atom

Yes, you are right. It is the problem of "atom_style charge". LAMMPS_EON.cpp sets "atom_style atomic" before reads in the in.lammps file.
by xph
Mon Aug 10, 2015 8:05 pm
Forum: eOn
Topic: "Unknown Potential: lammps" even though eonclient built with LAMMPS support
Replies: 4
Views: 10607

Re: "Unknown Potential: lammps" even though eonclient built with LAMMPS support

I followed the instruction on this page and it works now:
http://theory.cm.utexas.edu/eon/lammps_ ... -potential

The command to compile lammps library was updated:
make serial mode=lib
by xph
Mon Aug 10, 2015 2:52 am
Forum: eOn
Topic: Question about hyperdynamics/bond boost theory
Replies: 2
Views: 8256

Re: Question about hyperdynamics/bond boost theory

For the bb_dvmax, the ideal value is close to the lowest barrier height so that hyper potential energy surface (original plus bias) is as flat as possible. If bb_dvmax is set too high, it will prohibit efficiently sampling of boost factor in the reactant state. That means you may easily see a transi...
by xph
Thu Jul 09, 2015 4:59 pm
Forum: tsase
Topic: GPAW calculator in ss-dimer
Replies: 3
Views: 10302

Re: GPAW calculator in ss-dimer

The ssdimer module needs atoms.get_cell() and atoms.get_stresses(). If the calculator does not support stress calculation, the program dies when calling atoms.get_stresses().

Can you post the results of atoms.get_stresses() for these two modes?
by xph
Fri Jul 03, 2015 9:39 pm
Forum: tsase
Topic: GPAW calculator in ss-dimer
Replies: 3
Views: 10302

Re: GPAW calculator in ss-dimer

Usually the ss-dimer part is independent of the calculator. What is the difference between the two modes in GPAW? Do they both have the same format of stress in the output?
by xph
Tue Apr 14, 2015 9:43 pm
Forum: Bader
Topic: Bader charge vs. oxidation state
Replies: 4
Views: 10432

Re: Bader charge vs. oxidation state

I have seen that V(III) and V(IV) only differ in Bader charge by 0.08 to 0.15 depending on the local environment. See Table 2. on page 3093 of the following paper: http://theory.cm.utexas.edu/henkelman/pubs/xu14_3089.pdf The difference between O- and O2- is more obvious. The on-site occupancy or mag...
by xph
Sat Apr 04, 2015 9:08 pm
Forum: tsase
Topic: GPAW with TSASE
Replies: 3
Views: 10127

Re: GPAW with TSASE

In that case, you may want to push the initial guess a little further from the reactant minimum. It is better to start outside the concave region to get rid of those concerted mode.

In sum, try a better initial guess. At the same time, set a tighter rotation convergence: rotationMax = 20, phi_tol=3
by xph
Fri Apr 03, 2015 6:34 pm
Forum: tsase
Topic: GPAW with TSASE
Replies: 3
Views: 10127

Re: GPAW with TSASE

The dimer wouldn't stop if the curvature is positive. In your post, the last step (step 7) has a negative curvature. You can set a tighter convergence criteria, for example 0.03, to let the dimer run more steps. For the first few steps the curvature is positive and the force is small, which indicate...
by xph
Fri Dec 12, 2014 12:52 am
Forum: Bader
Topic: Charge transfer between two different orbitals in one atom
Replies: 3
Views: 6685

Re: Charge transfer between two different orbitals in one at

I think "charge transfer" here means charge distribution differences between Ni atom in the compounds and Ni atom in vacuum. If you already know the orbital occupations of isolated Ni atom, you just need to calculate the occupation numbers in the compound. For the density matrix, the diagonal number...
by xph
Mon Sep 01, 2014 6:21 pm
Forum: VTSTTools
Topic: problem in nebbarrier.pl, nebspline.pl and doslplot.pl
Replies: 4
Views: 7092

Re: problem in nebbarrier.pl, nebspline.pl and doslplot.pl

Currently, doslplot.pl only supports LORBIT=10.
To analyze LORBIT=11 results, the variable $col (column number to be printed) has to be adjusted in the script.
by xph
Fri Apr 04, 2014 3:42 am
Forum: VTSTTools
Topic: Is G-SSNEB available?
Replies: 12
Views: 14179

Re: Is G-SSNEB available?

Here we go. See the attachment for the example of the CdSe wurtzite to rock salt transition in a unit cell.

SSNEB is also available in TSASE, which is more handy: http://theory.cm.utexas.edu/henkelman/code/tsase.php
An example folder can be found when checked out.
by xph
Thu Mar 27, 2014 4:11 am
Forum: VTSTTools
Topic: The SS-NEB - external pressure set
Replies: 3
Views: 7841

Re: The SS-NEB - external pressure set

The initial and final structures are not changed during SSNEB calculations. OUTCARs are copied to these two folders, so it is not SSNEB's problem. But with PSTRESS, enthalpies in OSZICARs should be used instead of energies in OUTCARs in neb.dat. Be careful with nebbarrier.pl which reads energies fro...
by xph
Wed Aug 01, 2012 8:53 pm
Forum: VTSTTools
Topic: NEB distances in the MEP
Replies: 6
Views: 6569

Re: NEB distances in the MEP

The default is LCLIMB = True
You did not set LCLIMB = False, so these results are expected.