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Messages - markmick

Pages: [1] 2 3
1
General Questions and Answers / Export POSCAR: Cartesian and Direct
« on: August 10, 2016, 00:34 »
When I export a periodic slab to a poscar file, I get Direct coordinates, despite setting the Lattice Parameters and Coordinate List to Cartesian.  Why does it only come out Direct?

Thanks,
Mark

2
General Questions and Answers / Gibbs Free Energy and VASP
« on: August 9, 2016, 06:25 »
I've successfully performed binding energy calculations with VASP, but I'm stumped with Gibbs free energy.  Based on an article I'm studying, Gibbs Energy for an adsorbed hydrogen is calculated by:

ΔGH = ΔEH + ΔEZPE - TΔS

Some of these variables I understand, others I don't:

* T is temperature in Kelvin (Setting this in INCAR I believe)
* ΔS is entropy, which I believe is pulled from OUTCAR
* ΔEH  is the binding enegy, and I know how to do this one
* ΔEZPE (Zero-point-energy).  This one has me stumped. 

ΔEZPE  = ΔEnH - ΔE(n-1)H - 1/2 EH2

ΔEZPE has something to do with meV and THz values pulled from OUTCAR.  My INCAR is set with:

NELMIN = 4
ISMEAR = 0
IBRION = 7
ISIF = 0
LEPSILON = .TRUE.
NSW = 1
NWRITE = 3

and this produces an OUTCAR with final values like:

63 f  =    0.665149 THz     4.179253 2PiTHz   22.186976 cm-1     2.750835 meV

How to translate this OUTCAR data into the values for ΔEZPE elude me.  I assume just use the meV value?   Thanks for any assistance.  I'm accustomed to Gibbs from Thermodynamic calculations, but using VASP for this is a new frontier.

Sincerely,
Mark




 

3
General Questions and Answers / Computational Chemistry Importer?
« on: August 3, 2016, 04:48 »
What is the "Computational Chemistry Importer" in the LabFloor?  Couldn't find any documentation for this function.  It appears to parse NetCDF files,  But NetCDF's seem to be geographic data files, not molecular data.  Any insights?

Thanks,
Mark

4
General Questions and Answers / Re: Reciprocal space Hexagon K-points
« on: August 1, 2016, 21:49 »
Maybe I should ask the question differently.   When straining a lattice, I've seen two different ways of handling Kappa, as shown below.  Each returns very different results.  But which one is "correct"?   I need to see the change in the length between G-K and G-K', since strain will change k-space dimensions.  My gut reaction is Version 2, but I've seen folks insist on Version 1.  Version 1 is merely a mirror of K, not a different K. 

I need a second (or third) opinion on this for clarification.  I need KPOINTS that shows the difference in distance between G-K and G-K'.   My bandstructures for both of these versions are inconsistent.  Not sure which one I should focus on.

Version 1
0.333333 0.333333 0.000000  ! K
0.000000 0.000000 0.000000  ! G

0.000000 0.000000 0.000000  ! G
-0.333333 0.33333 0.000000  ! K'


Version 2
0.333333 0.333333 0.000000  ! K
0.000000 0.000000 0.000000  ! G

0.000000 0.000000 0.000000  ! G
-0.333333 0.666667 0.000000  ! K'

5
General Questions and Answers / Reciprocal space Hexagon K-points
« on: July 30, 2016, 08:08 »
For the 6 Kappa-points in a reciprocal space hexagon, can anyone clarify the values for those points, relative to Gamma?  I keep seeing different values in literature and vasp, and need this straightened out.  Based on my attached image, I believe the points (omitting the 0-value for z):

(1)  +0.333, +0.333
(2) +0.333, +0.667
(3) +0.333, -0.333
(4) -0.333, -0.333
(5) -0.333, -0.667
(6) -0.333, +0.333

Mark

6
General Questions and Answers / Strain, POSCAR's and KPOINTS
« on: July 28, 2016, 05:49 »
With VASP files, when applying uniaxial strain to a TMD, like MoS2, the POSCAR will change.  I can do this.  But does the reciprocal space path points in  KPOINTS also need to change? 

For example, the Kappa point of (1/3, 1/3, 0).  Should I leave the chosen KPOINTS path alone (G, M, K, G or whatever), or do I shift need to shift Kappa by the chosen strain amount? 

The high-symmetry points will change as the unit cell changes, but does VASP deal with that through the POSCAR, or does KPOINTS have to be shifted.  Hope this question makes sense.

Thanks,
Mark

7
General Questions and Answers / Gibbs Free Energy Calc
« on: July 17, 2016, 07:32 »
Can ATK determine Gibbs energy?  If so, how is it done and where does the value show up the Lab Floor?  I couldn't find any info in the tutorials, other than a mention that ATK can compute Gibbs.

Sincerely,
Mark

8
General Questions and Answers / BZ Viewer and Strain
« on: July 16, 2016, 22:17 »
The BZ Viewer is a very useful utility, however it's the first time I've experienced an interactive BZ and I'm having trouble interpreting the images.  I've read the "Uniaxial and biaxial stess in silicon" tutorial which has been helpful.

I attached an image with an unstrained  and strained MoS2.  There is degeneracy taking place as the atoms are shifted along the x-axis, but what other useful information can I extract from these images?   

Sincerely,
Mark

9
General Questions and Answers / Hydrogen Passivation
« on: July 10, 2016, 19:42 »
For unknown reasons, I cannot passivate the attached contcar with hydrogens.  I have plenty of other poscars where passivation works perfectly.  With this one, nothing happens.  I don't see anything abnormal about the file.  Any suggestions? I'm using 2016.b1 VNL.

Sincerely,
Mark

10
General Questions and Answers / DOS and weak/strong bond strength graphs
« on: June 6, 2016, 08:47 »
This is a physics question.  One goal of DOS is estimating bond strength of adsorbed species on a surface.  I'd like to see a sample of a DOS that shows weak bond strength and another that shows strong bond strength.  My physics and QM is rather weak, and DOS images would clarify the difference before I try to interpret the math. 

If I recall, I should be seeing more DOS filled below the Fermi level.  Am I on the right track?

Thanks,
Mark

11
General Questions and Answers / PDOS Properties "grayed out"
« on: May 8, 2016, 18:49 »
When I successfully open DOSCAR and display the PDOS image, the s,p,d, f shells are grayed out.  Is there an additional setting in VASP that I need to set?  I thought that LVTOT=True was all that was needed.

Mark

12
General Questions and Answers / Phonon Bandstructures and "strained" unit cells
« on: May 2, 2016, 23:57 »
I'm unable to create Phonon bandstructures Routes for "strained" unit cells.  I can successfully create them for unstrained poscars based on the Phonon Tutorial.

The PhononBandstructure scripter won't allow Routes beyond G.  I try to type in "G, M, K, G" and the text field prevents me from typing in anything other than G.  This makes sense I suppose, since the symmetry has been altered for strained unit cells.   But is there a work-around? 

Thanks,
Mark

13
General Questions and Answers / Re: POSCAR: Import-Export Issues
« on: May 1, 2016, 03:01 »
I have 2015.1 and still experiencing this issue.  Although the modified unit cell is technically correct, it crashes on VASP.  The "before" version runs perfectly fine on VASP, while the "after" version never converges, even after a 4-hour run.  How do I prevent VNL from changing the axis?

Mark

14
General Questions and Answers / POSCAR: Import-Export Issues
« on: April 29, 2016, 00:57 »
When I import the attached POSCAR-before file, the hexagonal unit cell immediately changes into another unit cell, that is then included when I Export the POSCAR.  I want to keep the original unit cell intact during Export. 

Is there an option to keep VNL from changing the unit cell?  The POSCAR-before file has the correct cell, and I want to keep that one, but I don't understand why VNL is changing it.

Thanks,
Mark

15
General Questions and Answers / Straining a Hexagonal Cell
« on: April 15, 2016, 23:49 »
I'm applying (uniaxial) strain to a Hexagonal unit cell for transition metal dichalcognides.  To change the Unit Cell, I had to manually modify the POSCAR file (since it's no longer a true Hexagonal lattice).  I tried "Stretch Cell", but that retains the symmetry.

Is there a way of straining the unit cell using VNL, so the lattice is changed in POSCAR?

Also, Reciprocal Space changes with strain.  KPOINTS should be equally strained, the routes don't change.  Can VNL modify the KPOINTS file to reflect strain on K-Space?  Otherwise, I have to do it manually.

0.000000 0.000000 0.000000 ! G
0.000000 0.500000 0.000000 ! M

0.000000 0.500000 0.000000 ! M
0.333333 0.333333 0.000000 ! K

0.333333 0.333333 0.000000 ! K
0.000000 0.000000 0.000000 ! G

Thanks,
Mark

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