Dear developers,
Hello.
I am now trying to get a z2-invariant using VASP code but I've got some problems in plotting the WCC using the Z2pack.
Firstly, I prepared the converged CHGCAR in advance and got WCC using the z2-implemented VASP code.
The material is Bi bulk structure. And this is what I got.
[image: image.png]
And this is the result provided in z2pack GitHub.
[image: image.png]
The main problem is where i made highlight with red circles. There are some condensed horizontal points that also middle point of largest gap (blue diamonds) are changed. In addition, the points near the two extreme x-axis ends are increased. Except for those, other points look very similar with z2pack provided result.
I've tested few options,
- pos_tol - move_tol - gap_tol - num_lines - min_neighbour_dist
however, they doesn't remove the condensed horizontal points.
Are there any ways/solutions that I can make a try?
------------------------------------------------------------------------------------ This the "run.py" I have used.
#!/home/woosun/Programs/Python3/bin/python3 import os import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import z2pack
# Creating the System. Note that the SCF charge file does not need to be # copied, but instead can be referenced in the .files file. # The k-points input is appended to the .in file # The command (mpirun ...) will have to be replaced to match your system. system = z2pack.fp.System( input_files=["input/CHGCAR", "input/INCAR", "input/POSCAR", "input/POTCAR", "input/wannier90.win" ], kpt_fct=z2pack.fp.kpoint.vasp, kpt_path="KPOINTS", command="mpirun /home/woosun/Source_codes/vasp544/vasp.5.4.4_for_z2/bin/vasp_ncl > stdout" )
if not os.path.exists('./results'): os.mkdir('./results') if not os.path.exists('./plots'): os.mkdir('./plots')
# Running the WCC calculation - standard settings result_0 = z2pack.surface.run( system=system, surface=lambda s, t: [0, s / 2, t], save_file = './results/res_0.p', load=True ) result_1 = z2pack.surface.run( system=system, surface=lambda s, t: [0.5, s / 2, t], save_file = './results/res_1.p', load=True )
# Plotting WCC evolution fig, ax = plt.subplots(1, 2, sharey=True, figsize = (9,5))
z2pack.plot.wcc(result_0, axis=ax[0]) z2pack.plot.wcc(result_1, axis=ax[1]) plt.savefig('plots/plot.pdf', bbox_inches = 'tight')
print('Z2 topological invariant at kx = 0: {0}'.format(z2pack.invariant.z2(result_0))) print('Z2 topological invariant at kx = 0.5: {0}'.format(z2pack.invariant.z2(result_1)))
------------------------------------------------------------------------------------
Thank you so much for reading the long email.
I will look forward to having your reply. :)
Sincerely, Jiwoo Lee.
Dear Jiwoo Lee,
From the plot it seems that your calculation contains many more Wannier charge centers than the reference example. Since the number of WCC corresponds to the number of bands considered by Wannier90, it seems likely that you need to change the "exclude_bands" input in the Wannier90 input file to only consider the 10 lowest bands.
A common cause for this issue is that VASP will automatically increase the number of bands if the initially specified number does not fit the number of cores. For example, if you run this calculation on a 32-core machine you might obtain 32 bands instead of the 15 specified in the NBANDS variable of the INCAR file. To adjust for that, you would have to then change the "exclude_bands" tag to "11-32" (instead of "11-15").
I hope this solves your problem, please don't hesitate to contact me again if it does not.
Best regards,
Dominik Gresch
On 28.01.19 08:18, 이지우 wrote:
Dear developers,
Hello.
I am now trying to get a z2-invariant using VASP code but I've got some problems in plotting the WCC using the Z2pack.
Firstly, I prepared the converged CHGCAR in advance and got WCC using the z2-implemented VASP code.
The material is Bi bulk structure. And this is what I got.
image.png
And this is the result provided in z2pack GitHub.
image.png
The main problem is where i made highlight with red circles. There are some condensed horizontal points that also middle point of largest gap (blue diamonds) are changed. In addition, the points near the two extreme x-axis ends are increased. Except for those, other points look very similar with z2pack provided result.
I've tested few options,
- pos_tol
- move_tol
- gap_tol
- num_lines
- min_neighbour_dist
however, they doesn't remove the condensed horizontal points.
Are there any ways/solutions that I can make a try?
This the "run.py" I have used.
#!/home/woosun/Programs/Python3/bin/python3 import os import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import z2pack
# Creating the System. Note that the SCF charge file does not need to be # copied, but instead can be referenced in the .files file. # The k-points input is appended to the .in file # The command (mpirun ...) will have to be replaced to match your system. system = z2pack.fp.System( input_files=["input/CHGCAR", "input/INCAR", "input/POSCAR", "input/POTCAR", "input/wannier90.win" ], kpt_fct=z2pack.fp.kpoint.vasp, kpt_path="KPOINTS", command="mpirun /home/woosun/Source_codes/vasp544/vasp.5.4.4_for_z2/bin/vasp_ncl > stdout" )
if not os.path.exists('./results'): os.mkdir('./results') if not os.path.exists('./plots'): os.mkdir('./plots')
# Running the WCC calculation - standard settings result_0 = z2pack.surface.run( system=system, surface=lambda s, t: [0, s / 2, t], save_file = './results/res_0.p', load=True ) result_1 = z2pack.surface.run( system=system, surface=lambda s, t: [0.5, s / 2, t], save_file = './results/res_1.p', load=True )
# Plotting WCC evolution fig, ax = plt.subplots(1, 2, sharey=True, figsize = (9,5))
z2pack.plot.wcc(result_0, axis=ax[0]) z2pack.plot.wcc(result_1, axis=ax[1]) plt.savefig('plots/plot.pdf', bbox_inches = 'tight')
print('Z2 topological invariant at kx = 0: {0}'.format(z2pack.invariant.z2(result_0))) print('Z2 topological invariant at kx = 0.5: {0}'.format(z2pack.invariant.z2(result_1)))
Thank you so much for reading the long email.
I will look forward to having your reply. :)
Sincerely, Jiwoo Lee.
-- *JIWOO LEE* | Research Associate Materials Theory Group | Department of Materials Science & Engineering 연세대학교 신소재공학과 재료 이론 연구실 통합과정 이지우
*YONSEI UNIVERSITY* 50 Yonsei-Ro | Seodaemun-Gu | 120-749 | Seoul | KOREA *M* +82-10-7282-5106 | *E* jiwoo2231@yonsei.ac.kr
mailto:jiwoo2231@yonsei.ac.kr | *W* http://www.materials-theory.org/
