Z2Pack

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52 discussions

Problem with tbmodel on python3.6.3
by Pham, Anh D. 16 Feb '19

16 Feb '19

Hi, I’m trying to install the tbmodel code with python3.6.3 and I have been getting this problem: UnicodeDecodeError: 'ascii' codec can't decode byte 0xc2 in position 49: ordinal not in range(128) Any help would be appreciated. Thanks, Anh

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[Questions for Z2pack] Dear developers,
by 이지우 28 Jan '19

28 Jan '19

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. -- *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(a)yonsei.ac.kr | *W* http://www.materials-theory.org/ -------------------------------------------------------------------------------------------------------------

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[Questions for Z2pack] Dear developers,
by 이지우 28 Jan '19

28 Jan '19

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. And this is the result provided in z2pack GitHub. 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(a)yonsei.ac.kr | *W* http://www.materials-theory.org/ -------------------------------------------------------------------------------------------------------------

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topological invariants calculation on 2D system
by Yifan GAO 28 Sep '18

28 Sep '18

Hello, I don't quite understand how can I get the topological invariants, like Z2 and Chern, within a 2D system? I'm feeling puzzled when building the surface. BTW I'm using vasp. Thank you, Patric

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PosCheck test under Line Convergence Fails
by Zeeshan Ahmad 17 May '18

17 May '18

Hi Z2pack users, I have a question about obtaining convergence for the Z2 invariant of 2D system (30 angstrom vacuum) I am running (kz=0). My convergence report is: +----------------------------------------------------------------------+ | ================== | | CONVERGENCE REPORT | | ================== | | | | Line Convergence | | ================ | | | | PosCheck | | -------- | | PASSED: 16 of 21 | | FAILED: 5 of 21 | | | | Surface Convergence | | =================== | | | | GapCheck | | -------- | | PASSED: 20 of 20 | | | | MoveCheck | | --------- | | PASSED: 20 of 20 | +----------------------------------------------------------------------+ with these settings: result_0 = z2pack.surface.run( system=system, surface=lambda s, t: [s / 2, t, 0], save_file='./results/res_0.json', load=True, iterator = (20,151,2)#,min_neighbour_dist=1e-6, num_lines = 201 ) I also tried changing the min_neighbor_dist to 1e-6 and num_lines to 201, but still could not obtain convergence in PosCheck. I’d be grateful if you could share any tips for obtaining convergence. Thanks, -Zeeshan -- Zeeshan Ahmad PhD candidate Carnegie Mellon University

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Error installing Z2Pack 2.1.1
by Rajdeep Banerjee 16 Apr '18

16 Apr '18

Hi, I am trying to install Z2Pack 2.1.1 (from source file). I am getting the following error: Downloading/unpacking fsc.export (from z2pack==2.1.1) Downloading fsc.export-1.1.0.tar.gz Running setup.py (path:/tmp/pip_build_rajdeep/fsc.export/setup.py) egg_info for package fsc.export error in fsc.export setup command: Invalid environment marker: python_version < "3" Complete output from command python setup.py egg_info: error in fsc.export setup command: Invalid environment marker: python_version < "3" ---------------------------------------- Cleaning up... Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_rajdeep/fsc.export Storing debug log for failure in /tmp/tmp3bth1l3g I thought it is due to python version but I have python 3.5 as shown below: [rajdeep@anna: Z2Pack-master-2.1.x]:python Python 3.5.3 (default, Apr 22 2017, 00:00:00) [GCC 4.8.4] on linux Type "help", "copyright", "credits" or "license" for more information. >>> Please help. Thanks in advance! best regards, -- Rajdeep Banerjee PhD student JNCASR, Bangalore India

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Mirror Chern number for SnTe
by raagya＠jncasr.ac.in 02 Apr '18

02 Apr '18

Respected Sir/Maam, I am a student of JNCASR, Bangalore, India and working on SnTe system. Can you help me in calculating the mirror chern number for SnTe system using Z2 pack software and Quantum espresso. I have calculated the Z2 topological index for SnTe but and in order to study the system I need to focus on mirror chern number as you have shown in the following paper. [ https://journals.aps.org/prb/pdf/10.1103/PhysRevB.95.075146 | https://journals.aps.org/prb/pdf/10.1103/PhysRevB.95.075146 ] (Page 10 of this paper SnTe mirror chern number has been calculated). Can you please help me with the steps in order to calculate the mirror chern number for SnTe system? Thanking you, With warm regards, Raagya Arora JNCASR, Bangalore India

1 0

question about z2pack
by Qian Yuting 27 Feb '18

27 Feb '18

Hello Dominik, Recently I try to learn z2pack. I used it to calculate the Z2 invariants of Bi and Bi2Se3 and found it's really a very good tool! Then I want to apply it to calculate the chirality of wey points using vasp. But after I use it , it encountered a problem: “File "/home/qian/.local/lib/python3.6/site-packages/z2pack/fp/kpoint.py", line 189, in _check_equal_spacing raise ValueError('The k-points must be equally spaced for {} runs.'.format(run_type)) ValueError: The k-points must be equally spaced for VASP runs.” How can I solve this problem ? Does that mean z2pack can 't calculate the chirality using vasp? Looking forward to your reply ! Thank you in advance. Best regards, Yuting Qian ---------- Yuting Qian EPFL at Swizerland, & Institute of Physics, Chinese Academy of Science,Beijing,China yuting.qian(a)epfl.ch

1 0

Please help me to clarify the mentioned points
by Majeed Ur Rehman 28 Dec '17

28 Dec '17

Respected Sir/Madam I am Mr.Majeed Ur Rehman from Pakistan. I am Master student with very less background in VASP. Currently, i am learning vasp tools. These days i am interested to learn how one can calculate a Berry curvature and Z2 topological index using vasp, wannier90. Let me mention that wannier90 and Z2 pack are already interfaced with the VASP on our cluster. But the problem is to how can I use it to calculate Berry curvature and Z2 topological index. For this, I need some guideline from an expert like you, because no expert is available here with me to guide. Your help would be highly appreciated. I know you would be too much busy sir but your help would be like an oxygen for me to survive at this initial and difficult stage of my learning. Thank You and looking forward for your nice response. Best Regards Majeed-Ur-Rehman

2 1

Z2 invariant for 2D material (or a semi-infinite slab)
by koushik pal 24 Nov '17

24 Nov '17

Hello All, I was wondering if it's possible to calculate Z2 invariant for a 2D material (or a semi-infinite slab) using the Z2Pack code. Let's say I have a slab model with (001) surface orientation (i.e. vacuum is along the z-direction of the slab). To determine the topological invariant of this (001) slab, shall I calculate the Z_2 invariant for kz=0 and kz=0.5 planes, and take their difference modulo 2? The problem here is the following. As this is a slab, kz=0.5 plane does not have any physical meaning. So I don't know if Z2 invariant on kz=0.5 plane has some significance. Please correct me if I am missing something here, and suggest me ways to calculate Z2 invariant for such a slab. Thanks in advance. Best regards, Koushik Graduate student JNCASR Bangalore, India

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