[Wannier] Centre of Wannier functions

Fri Jun 7 14:21:18 CEST 2024

Hi, I don't think there is a very simple solution by just changing some code flags.

My suggestion would be, assuming (as it should be) that you have as small tilmestep in your MD, that you post-process the data and shift at every step all WFs by integer lattice vectors, so as to keep their position as "continuous" as possible (essentially, given a WF center at step i, you look for all possible replicas by shifting by lattice vectors e.g. in a small supercell, and find the closest one to the corresponding WF in MD step (i-1), and consider that as the WF position).

Best,
Giovanni

On 7 Jun 2024, at 10:58, 李滕辉 <lith at zju.edu.cn> wrote:

Dear Wannier90 developers:
I meet an issue while using Wannier90 v3.1.0, together with VASP v6.4.1. I've done some AIMD calculations to generate a continuous trajectory. Then I proceeded with Wannier analysis and subsequently examined the Hamiltonian. Within the input file, I have specified the atom centers, aiming to obtain WFs centered on these atom locations, or at least in close proximity to them.

...
Begin Projections
 Cd:sp3:z=-1,-1,-1,x=1,0,-1
 Se:p:z=-1,-1,-1,x=1,0,-1
End Projections
...
begin unit_cell_cart
     6.0500000     0.0000000     0.0000000
     0.0000000     6.0500000     0.0000000
     0.0000000     0.0000000     6.0500000
end unit_cell_cart
begin atoms_cart
Cd       1.5178271     1.7957993     1.4240287
Cd       4.4307325     4.4894561     1.7053815
Cd       4.5160066     1.2418392     4.5483831
Cd       1.5803075     4.4594387     4.5691762
Se       0.0050033     0.0332671     5.9680866
Se       6.0433290     3.0636897     3.0562890
Se       2.8807786     0.0724863     3.0164791
Se       3.2493695     3.0420933     5.8999131
end atoms_cart
...

However, I have observer that the WFs are not aligning with the atom centers of the home cell. Instead, they are centered on atoms within a unit cell whose center is located at(0.0, 0.0, 0.0). For instance,  since I use sp3 orbitals for Cd, the center of WF5 corresponds to the second Cd atoms, while the atom center positioned at (4.43. 4.49. 1.71) and the WF center at (-1.01, -2.12, 1.14) in the .wout file.

...
 Final State
  WF centre and spread    1  (  2.085684,  1.260598,  0.798043 )     3.47876053
  WF centre and spread    2  (  2.049201,  2.344944,  1.921311 )     3.44168714
  WF centre and spread    3  (  0.904277,  1.241577,  1.954697 )     3.43610592
  WF centre and spread    4  (  1.042490,  2.326357,  0.905988 )     3.58232243
  WF centre and spread    5  ( -1.010143, -2.123145,  1.141211 )     3.49051492
  WF centre and spread    6  ( -1.128292, -0.972610,  2.258101 )     3.52243681
  WF centre and spread    7  ( -2.121837, -2.038340,  2.220324 )     3.46813098
  WF centre and spread    8  ( -2.218949, -1.012121,  1.103897 )     3.51827962
  WF centre and spread    9  ( -1.015362,  0.681962, -2.070276 )     3.60904653
  WF centre and spread   10  ( -0.890789,  1.882241, -0.973578 )     3.63289332
  WF centre and spread   11  ( -2.108611,  0.719542, -0.996879 )     3.46637567
  WF centre and spread   12  ( -2.115134,  1.897953, -2.162619 )     3.66683836
  WF centre and spread   13  (  2.150342, -2.128650, -2.068309 )     3.51187251
  WF centre and spread   14  (  2.156870, -1.008390, -0.926044 )     3.53284787
  WF centre and spread   15  (  1.050800, -2.157773, -0.945039 )     3.46859217
  WF centre and spread   16  (  0.958142, -1.003749, -2.060564 )     3.59315863
  WF centre and spread   17  (  0.037244,  0.001632, -0.049092 )     2.50422447
  WF centre and spread   18  (  0.015322,  0.080868, -0.134619 )     2.21017329
  WF centre and spread   19  ( -0.059586,  0.030045, -0.095360 )     2.28365022
  WF centre and spread   20  (  0.037435, -3.029794, -2.977580 )     2.46391151
  WF centre and spread   21  (  0.000015, -2.932250, -3.012771 )     2.31121349
  WF centre and spread   22  ( -0.056325, -2.986181, -2.999162 )     2.38773168
  WF centre and spread   23  (  2.893882,  0.030034,  3.037144 )     2.38000522
  WF centre and spread   24  (  2.928631,  0.123782,  2.984530 )     2.38126096
  WF centre and spread   25  (  2.821335,  0.075610,  3.032140 )     2.43241519
  WF centre and spread   26  ( -2.791587, -3.058092, -0.116545 )     2.45592149
  WF centre and spread   27  ( -2.744926, -2.945582, -0.212516 )     2.32087924
  WF centre and spread   28  ( -2.851460, -3.004112, -0.153946 )     2.45045905
  Sum of centres and spreads (  0.018668,-17.703645, -0.597512 )    85.00170923
...

While this discrepancy does not present an issue in static calculations, it becomes problematic in MD trajectories. For instance, When an atom moves from (0, 0, 0.49) to (0, 0, 0.51), the center shifts from (0, 0, 0.49) to (0, 0, -0.49), resulting in a discontinuity in the Hamiltonian non diagonal element indices.

I've made attempts to address this issue by adjusting parameters in the .win file, such as setting translate_home_cell = true, or explicitly setting the center of each orbital. But none of them works. It seems that the WF centres are predetermined in ab initial calculations. Therefore, I am reaching out to inquire if there exist specific parameters or solutions to solve this problem.

Thank you for your attention and assistance.

Best regards,
Tenghui Li
Department of Chemistry, Zhejiang University, China
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