Messages

1

General Questions and Answers / Re: Calculate conduction bands of different layers in atk

« on: August 17, 2017, 11:12 »

Ok, thanks for the suggestion. Is it not possible to extract it just from the dos of the individual layer?
I just want to know the homo and lumo for the individual layers.
 

You can project the band structure on a subset of atoms when you set up the band structure calculation.

2

General Questions and Answers / Calculate conduction bands of different layers in atk

« on: August 16, 2017, 19:36 »

Hi,

I have a multilayered system with vacuum on top. I calculated dos for the system, and I can see, depending on the fermi energy, where my conduction
and valence bands lie. Can someone tell me how I can calculate the CBM and VBM for different layers in a layered structure?
Can I extract it from the graph just by selecting the individual layers in atk?

Thanks

3

General Questions and Answers / Re: Too much expansion of the unit cell : ReTe2

« on: June 25, 2017, 18:34 »

Thanks for the suggestions. I will try them.

4

General Questions and Answers / Re: Too much expansion of the unit cell : ReTe2

« on: June 23, 2017, 18:48 »

Thanks for your response.

@Petr I guess then I should keep it fixed (bravais lattice and z-direction) all throughout even when I am modelling interactions of molecules with ReTe2 (?) since I don't wish to obtain a new phase as a result of interactions. I am interested in total energy calculations.

5

General Questions and Answers / Too much expansion of the unit cell : ReTe2

« on: June 22, 2017, 18:27 »

Hi,

I have a ReTe2 unit cell with 20 Ang vacuum on top. I would like to analyze monolayer properties by geometry optimization.
My parameters are 0.01 ev/Ang max_force and 0.001 ev/Ang3 max_stress. As per one of the (atk forum) posts, 0.001 is good as a stress value. I use GGA, PBE with DFT-D3 correction. xyz directions are free to move and bravais lattice is unconstrained. Isotropic pressure = 0 is used. I found that after optimization, the unit cell has expanded a lot. The total z direction now stands at 42 Ang. Is it normal given the above optimization conditions? I see the same for some other materials as well. What could lead to such a high expansion? I was assuming that 20 Ang vacuum should be enough to avoid z-direction expansion. I was intially planning to fix z-direction but clearly that would have given me incorrect results (?). If I use a supercell for further study, I would have to deal with a huge cell. Any work around? Does it make sense to fix the z-direction now for the supercell to study interaction with molecules?

Thanks

6

General Questions and Answers / Re: Force and stress tolerances for 2D monolayer optimization

« on: June 21, 2017, 22:09 »

Thanks for the reply. Yes, I guess a benchmark would be helpful. I was just hoping that there should be some general settings
that I can use safely specially in the context of supercells (maybe a lower restraint).

Thanks for your input.

7

General Questions and Answers / Re: Force and stress tolerances for 2D monolayer optimization

« on: June 21, 2017, 11:27 »

Hi,
Thank you for your reply.

I have given the parameters in my question. When I asked this question my main concern was If I can go for a higher stress and force settings to improve time.The unit cells in most cases consist of 3 atoms (take MoS2 for example) and can be obtained from materials project. Inside geometry optimization I use 0.01eV/Ang max_force, 0.001 eV/Ang max_stress. Steps 200 and nothing is constrained (neither x,y,z nor bravais lattice). I guessed that the cut-offs above are already rigorous so that shouldn't be a problem. One thing to clarify though that the supercells are very large (8x8x1). As far as I have read in journals, people don't use such large cells (mostly 5x5x1 supercells). I had to use bigger for consistency and because of previous experiences with certain materials. So using 1x1x1 k points for supercells won't be a problem. In case of single unit cells it will cause problems and ATK detects that I should use 4x3x1 k-points in general, but to be safe across all materials I go with 5x5x1 k-points (With 20 Ang vacuum, the z direction is way too big to use more k points. Of course I can use but I shouldn't have to). Other settings in Geometry optmization are standard LBFGS and 0.2 Ang step size.


Thanks

8

General Questions and Answers / Force and stress tolerances for 2D monolayer optimization

« on: June 20, 2017, 17:30 »

Hi,

I have to optimize multiple supercells and I am wondering if I can follow some guidelines in deciding parameters that can
quickly(reasonably) optimize the systems. I have optimized the unit cells of various 2D materials monolayers with large enough
vacuum (almost 20 Angstrom) on top. When I optimize the supercells now with max_force = 0.01ev/Ang and max_stress=0.001eV/Ang3(same as for unit cells), I find that the supercell made of optimized unit cell still takes quite some time to finish. Since the 2D materials consist of different metals and chalcogens, is there a safe cut-off that can help optimize the supercells rather quickly? Say max_force=0.05 and max_stress=0.05? Will it ber reasonable? I want to calculate total energies in the end and later dos.  K points used are 1x1x1 (for unit cells it was 5x5x1). GGA.PBE with vdW correction and DZP basis is used. Can I fix the z coordinate for supercells to save time in relaxation? I didn't do it earlier because sometimes (for some systems) I see the z direction change during relaxation even with 20 Ang vacuum. Since this is just a first step and later  I have to model interactions of molecules with these monolayers, I would like to find a way that can give reasonably accurate energies and save time.

Thanks for your inputs.

9

General Questions and Answers / Re: Calculation of stability SnS

« on: May 7, 2017, 18:04 »

I tried increasing the cutoff to 200 Hartree and also changed the limits for force and stress tolerances to 0.001 and 0.0001 respectively.
Everything else remains the same (2015 version as I don't have 2016) GGA -PBE, DFT-D3. The 62 structure alpha phase converges while 63 runs into an error pasted below:

Traceback (most recent call last):
  File "SnS_63_orig.py", line 76, in <module>
    optimizer_method=LBFGS(),
  File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 331, in OptimizeGeometry
  File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 497, in runSimultaneousRelaxation
  File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 401, in runRelaxation
  File "./zipdir/NL/Dynamics/Optimization/OptimizerMethod.py", line 502, in step
  File "./zipdir/NL/Dynamics/StrainFilter.py", line 133, in set_positions
  File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 243, in _updateCell
  File "./zipdir/NL/CommonConcepts/Configurations/ConfigurationCopy.py", line 145, in stretchRelaxationCell
  File "./zipdir/NL/CommonConcepts/Configurations/ConfigurationCopy.py", line 113, in newLatticeFromCell
  File "./zipdir/NL/CommonConcepts/Configurations/BravaisLattice.py", line 1970, in __init__
  File "./zipdir/NL/CommonConcepts/Configurations/BravaisLattice.py", line 1311, in __init__
  File "./zipdir/NL/CommonConcepts/Configurations/BravaisLattice.py", line 194, in checkValidLength
NL.ComputerScienceUtilities.Exceptions.NLValueError: The lattice parameter a must be larger than 0*Units.Ang


What could possibly lead to 0*Units.Ang ?

Thanks

10

General Questions and Answers / Re: Calculation of stability SnS

« on: May 7, 2017, 12:47 »

Thanks Ulrik for your reply. Indeed the difference is too small. I am using GGA-PBE with double zeta polarized basis. I will try as suggested. By job manager I meant the window where we see all the queued or running jobs. There I saw that the job status is done but when I clicked the log option just beside it, I found that the job was not finished. No calculations were in progress though. Maybe the log was not written anymore. Anyway, it's not a recurring problem and happened only once. Thanks for your suggestion.

11

General Questions and Answers / Calculation of stability SnS

« on: May 5, 2017, 12:00 »

Hello all,

I am a new user in the quantumwise community, so please accept my greetings.

Starting with the main business, I would like to ask how I can evaluate the stability of
materials using quantumwise? I have two structures taken from materialsproject website
for SnS bulk (62 pnmahttps://materialsproject.org/materials/mp-2231/
and
63 cmcmhttps://materialsproject.org/materials/mp-559676/ group). I see on the website that the
62 structure (alpha phase) is more stable if we look at the energies per atom.
I wanted to obtain the same conclusion using GGA functionals, but I always find that beta is slightly
more stable than alpha. I did Geometry optimization using high kpoints (9x9x9 and 13x13x13)
with PBE and PBES. Even though the energy difference is smaller on the website as well, it does
mention that 63 decomposes to 62. I also use DFTD2 corrections. Can someone point out why
this could be happening?

Additional note: I left the simulations to compelte overnight. Next day the logs still show that
                        some part of the calculations are still being evaluated while the jobmanager show
                        that they are done. Using version 2014.1. While this has nothing to do with the results
                        as even if logs are ok, the calculations are still the same.

Thanks in advance for your suggestions.