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Topics - faxer92

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1
Dear Prof.
I followed tutorials of Silicon and tried building my own InSe TB model, however, I didn't completely catch physical meaning in Silicon case, its about determination of occupations in spds* basis and orbital-chosen in hatree potentials. For example, Bassani's parameters of As atom in library(basis: spds*) do not show same Si occupation of # number_of_valence_electrons = 4, occupations= [0.4, 1.2, 2.0, 0.4] in other elements?  if so how to attain, e.g. As, occupations=[ 1.577 , 3.012 , 0.204 , 0.067 ]?

arsenic_onsite_term = SlaterKosterOnsiteParameters(
    element=PeriodicTable.Arsenic,
    angular_momenta=[ 0 , 1 , 2 , 0 ],
    occupations=[ 1.577 , 3.012 , 0.204 , 0.067 ], <====Q1.
    filling_method=SphericalSymmetric,
    ionization_potential=[ -5.9801*eV , 3.5813*eV , 12.1954*eV , 17.8411*eV ],
    onsite_hartree_shift=[ 7.81664*eV , 7.81664*eV , 7.81664*eV , 7.81664*eV ], <====Q2
    onsite_spin_split=[[-0.619, -0.43145, -0.43145, -0.619], [-0.43145, -0.3804, -0.3804, -0.43145], [-0.43145, -0.3804, -0.3804, -0.43145], [-0.619, -0.43145, -0.43145, -0.619]]*eV,
    onsite_spin_orbit_split=[0.0, 0.3526, 0.0, 0.0]*eV,     <=====Q3
    vacuum_level=0.0*Hartree,
    )

Second and third Quiz is. Why/How hartree or spin_split are determined by[ "?p", "?p", "?p", "?s"]
instead of basis assumption of ["3s", "3p", "3d", "3s"] in ionization_potential, and how to read ["3p"], 'ncp' in Si tutorials?
+++++++++++++++++++++++++++++++++++++++++++++
onsite_hartree_shift=ATK_U(PeriodicTable.Silicon, ["3p"], 'ncp')[0],
onsite_spin_split=ATK_W(PeriodicTable.Silicon, [ "3p", "3p", "3p", "3s" ]),
+++++++++++++++++++++++++++++++++++++++++++++

thank you for your kind assistance and waiting for your reply

2
Dear QW Experts,

How to sequentially run jobs from test1.py to test10 in atk (qsub in cluster system)?   
for example,

~/libexec/ mpiexec.hydra -machinefile MachineFile -n 24 ~/bin/atkpython test1.py 2>&1 | tee test1.log

~/libexec/ mpiexec.hydra -machinefile MachineFile -n 24 ~/bin/atkpython test2.py 2>&1 | tee test2.log

......

~/libexec/ mpiexec.hydra -machinefile MachineFile -n 24 ~/bin/atkpython test10.py 2>&1 | tee test10.log

thank you so much and appreciate of your concern. ;)

3
Hi, ATK experts,
When computing surface energy, it's very easy to hit dipole polarization in slab.
In VASP, people can correct this dipole issue by setting interior function (-LDIPOL).
But, how to overcome this issue in ATK?
A  symmetric mirror-slab method is often proposed in ancient papers,
https://www.researchgate.net/post/How_do_I_avoid_polarization_in_surface_energy_calculation_using_DFT
how to apply this in my case, i.e., asymmetric structure of o-phase HfO2.
much appreciate for your assistance.

===========================
data_global
_cell_length_a 5.23
_cell_length_b 5.04
_cell_length_c 5.06
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_symmetry_space_group_name_H-M 'P -1'
loop_
_symmetry_equiv_pos_as_xyz
  'x,y,z'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Hf 0.968 0.733 0.743
Hf 0.468 0.267 0.743
Hf 0.032 0.267 0.243
Hf 0.532 0.733 0.243
O 0.111 0.068 0.888
O 0.389 0.068 0.388
O 0.611 0.932 0.888
O 0.889 0.932 0.388
O 0.733 0.463 0.992
O 0.767 0.463 0.492
O 0.233 0.537 0.992
O 0.267 0.537 0.492

4
Dear Sir
when I test run program at link https://docs.quantumwise.com/manuals/Types/FHIaimsCalculator/FHIaimsCalculator.html
it shows no matching license as follows:

License Error: (Internal: 455 Feature: ATKFHIaims)

[LOCAL] /home/xxxxxx/.quantumwise/licenses/a-xxxx-qw2017.lic - (Err: 51) Unable to use network license as a local license
[NETWORK] 6200@localhost - (Err: 9) Feature not found
[NETWORK] 6200@localhost - (Err: 9) Feature not found
[NETWORK] 6200@localhost - (Err: 9) Feature not found
[NETWORK] 6200@localhost - (Err: 9) Feature not found

License configuration (environment variables):
---------------------------------------------------------------------------
QUANTUM_LICENSE_PATH = ':/home/xxxxx/.quantumwise/licenses:6200@localhost:6200@localhost:6200@localhost'
---------------------------------------------------------------------------
*** Make sure to include the information above when contacting support ***

For assistance on resolving this matter, there are several options:
  Consult the FAQ             : http://quantumwise.com/support/faq
********
In the morning, I reported this event to my local agency, Annie, a superior  Pitotech corp's employee , she checked and
also confused at this license issue, explained she had issued the complete ATK to us in last march, 2017(purchase).
For this, she kindly pass my information to you, and suggest me to report to you to get quick answer.
Could you please kindly help us check this problem ASAP since I'm going to report in a forum in Hawaii, and need
benchmark  FIHAIM potential with others, and I believe FIHAIM would be a discussion point after my session.

Much appreciate for your assistance
Best, Ethan  ;)

ps. license file can be followed in Annie's mail
thanks again

5
Dear Sirs
Last weekend I hit 3 issue in ATK mpi settings. The story is when I used 36 core to run the following script, it's quickly converged at 37 step in each loop. However, as increasing computing process to 44 core from 36,  which gives not converged results, even >100 steps? Same code gives very different results due to process number setting, could you please explain this ? The second bizarre thing is,  my cluster is made of A(44 core/256G ram)+B(14 core/128G ram), when I turn off B and run web example mpi_test.py with mpi "58" process in only A, which equally showing 1 master+57 slaves (completely ignores my physical cpu number is 44 ea in A) and keeps running, why?  does ATK may virtualize cpu/process in A ? What's the correct concept between process and physical cpu count in ATK? Could you hint me where I  shall improve? much appreciate and looking forward to your replies.   

--------------
The third bizarre is : I have physical 14 cpu in B, but fully running program with mpi: 58,  they always shows 0% performance , anything wrong in my QW path setting or folders in clstr?

6
Questions and Answers / How to build this cell?
« on: October 28, 2017, 10:59 »
Dear sirs, in this case, since all xyz is a complex  combination of  abc,  how can I make it in Builder in ATK? what's the difference  in choice S/Z in space group  #137?

7
Dear masters
Is it possible to define a inner square boundary via voronoi builder?
thank you so much

8
Dear Sir
When execute Prof. Blom's code "cb_plot.py" from
http://quantumwise.com/forum/index.php?topic=3376.0
 I get an error:

File ".\build\lib\site-packages\matplotlib-1.5.0-py2.7-win-amd64.egg\matplotlib\mlab.py", line 3421, in griddata
RuntimeError: To use interp='nn' (Natural Neighbor interpolation) in griddata, natgrid must be installed. Either install it from http://github.com/matplotlib/natgrid or use interp='linear' instead.

how to I do to make it work?
Regards

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