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Hi, I don't think there is a very simple solution by just changing some code flags.
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<div>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).</div>
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<div>Best,</div>
<div>Giovanni</div>
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<blockquote type="cite">
<div>On 7 Jun 2024, at 10:58, 李滕辉 <lith@zju.edu.cn> wrote:</div>
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Dear Wannier90 developers:
<div>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.</div>
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<div style="margin: 0px;">...</div>
<div style="margin: 0px;">Begin Projections</div>
<div style="margin: 0px;"> Cd:sp3:z=-1,-1,-1,x=1,0,-1</div>
<div style="margin: 0px;"> Se:p:z=-1,-1,-1,x=1,0,-1</div>
<div style="margin: 0px;">End Projections</div>
<div style="margin: 0px;">...</div>
<div style="margin: 0px;">begin unit_cell_cart</div>
<div style="margin: 0px;"> 6.0500000 0.0000000 0.0000000</div>
<div style="margin: 0px;"> 0.0000000 6.0500000 0.0000000</div>
<div style="margin: 0px;"> 0.0000000 0.0000000 6.0500000</div>
<div style="margin: 0px;">end unit_cell_cart</div>
<div style="margin: 0px;">begin atoms_cart</div>
<div style="margin: 0px;">Cd 1.5178271 1.7957993 1.4240287</div>
<div style="margin: 0px;">Cd 4.4307325 4.4894561 1.7053815</div>
<div style="margin: 0px;">Cd 4.5160066 1.2418392 4.5483831</div>
<div style="margin: 0px;">Cd 1.5803075 4.4594387 4.5691762</div>
<div style="margin: 0px;">Se 0.0050033 0.0332671 5.9680866</div>
<div style="margin: 0px;">Se 6.0433290 3.0636897 3.0562890</div>
<div style="margin: 0px;">Se 2.8807786 0.0724863 3.0164791</div>
<div style="margin: 0px;">Se 3.2493695 3.0420933 5.8999131</div>
<div style="margin: 0px;">end atoms_cart</div>
</div>
<div>...</div>
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<div>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<span class="Apple-converted-space"> </span><em>sp<sup>3</sup></em><sup><span class="Apple-converted-space"> </span></sup>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.</div>
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<div>...</div>
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<div style="margin: 0px;"> Final State</div>
<div style="margin: 0px;"> WF centre and spread 1 ( 2.085684, 1.260598, 0.798043 ) 3.47876053</div>
<div style="margin: 0px;"> WF centre and spread 2 ( 2.049201, 2.344944, 1.921311 ) 3.44168714</div>
<div style="margin: 0px;"> WF centre and spread 3 ( 0.904277, 1.241577, 1.954697 ) 3.43610592</div>
<div style="margin: 0px;"> WF centre and spread 4 ( 1.042490, 2.326357, 0.905988 ) 3.58232243</div>
<div style="margin: 0px;"> WF centre and spread 5 ( -1.010143, -2.123145, 1.141211 ) 3.49051492</div>
<div style="margin: 0px;"> WF centre and spread 6 ( -1.128292, -0.972610, 2.258101 ) 3.52243681</div>
<div style="margin: 0px;"> WF centre and spread 7 ( -2.121837, -2.038340, 2.220324 ) 3.46813098</div>
<div style="margin: 0px;"> WF centre and spread 8 ( -2.218949, -1.012121, 1.103897 ) 3.51827962</div>
<div style="margin: 0px;"> WF centre and spread 9 ( -1.015362, 0.681962, -2.070276 ) 3.60904653</div>
<div style="margin: 0px;"> WF centre and spread 10 ( -0.890789, 1.882241, -0.973578 ) 3.63289332</div>
<div style="margin: 0px;"> WF centre and spread 11 ( -2.108611, 0.719542, -0.996879 ) 3.46637567</div>
<div style="margin: 0px;"> WF centre and spread 12 ( -2.115134, 1.897953, -2.162619 ) 3.66683836</div>
<div style="margin: 0px;"> WF centre and spread 13 ( 2.150342, -2.128650, -2.068309 ) 3.51187251</div>
<div style="margin: 0px;"> WF centre and spread 14 ( 2.156870, -1.008390, -0.926044 ) 3.53284787</div>
<div style="margin: 0px;"> WF centre and spread 15 ( 1.050800, -2.157773, -0.945039 ) 3.46859217</div>
<div style="margin: 0px;"> WF centre and spread 16 ( 0.958142, -1.003749, -2.060564 ) 3.59315863</div>
<div style="margin: 0px;"> WF centre and spread 17 ( 0.037244, 0.001632, -0.049092 ) 2.50422447</div>
<div style="margin: 0px;"> WF centre and spread 18 ( 0.015322, 0.080868, -0.134619 ) 2.21017329</div>
<div style="margin: 0px;"> WF centre and spread 19 ( -0.059586, 0.030045, -0.095360 ) 2.28365022</div>
<div style="margin: 0px;"> WF centre and spread 20 ( 0.037435, -3.029794, -2.977580 ) 2.46391151</div>
<div style="margin: 0px;"> WF centre and spread 21 ( 0.000015, -2.932250, -3.012771 ) 2.31121349</div>
<div style="margin: 0px;"> WF centre and spread 22 ( -0.056325, -2.986181, -2.999162 ) 2.38773168</div>
<div style="margin: 0px;"> WF centre and spread 23 ( 2.893882, 0.030034, 3.037144 ) 2.38000522</div>
<div style="margin: 0px;"> WF centre and spread 24 ( 2.928631, 0.123782, 2.984530 ) 2.38126096</div>
<div style="margin: 0px;"> WF centre and spread 25 ( 2.821335, 0.075610, 3.032140 ) 2.43241519</div>
<div style="margin: 0px;"> WF centre and spread 26 ( -2.791587, -3.058092, -0.116545 ) 2.45592149</div>
<div style="margin: 0px;"> WF centre and spread 27 ( -2.744926, -2.945582, -0.212516 ) 2.32087924</div>
<div style="margin: 0px;"> WF centre and spread 28 ( -2.851460, -3.004112, -0.153946 ) 2.45045905</div>
<div style="margin: 0px;"> Sum of centres and spreads ( 0.018668,-17.703645, -0.597512 ) 85.00170923</div>
<div>...</div>
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<div>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.</div>
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<div>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.</div>
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<div>Thank you for your attention and assistance. </div>
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<div>Best regards,</div>
<div>Tenghui Li</div>
<div>Department of Chemistry, Zhejiang University, China</div>
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