Z2Pack

z2pack@lists.phys.ethz.ch

52 discussions

General setup for Vasp
by 朱家铎 07 Apr '17

07 Apr '17

Dear sir, I would like to calculate z2 invariants of a 2D system under VASP. There are a few issues, which confused me. 1. I tried the example of Bi for vasp. But SOC needs more bands than the posted INCAR which contains only 15 bands. So, the results never comes out. And I am also confused the exclude bands in the wannier90.win, because the fermi level can be pined by the Dirac cones usually. In this case, I would like to know if it is correct to exclude the higher energy band of the Dirac cone? 2. The KPOINTS setup is always 1 1 7 (I followed examples of Bi) , Is there suggestions for the correct k-mesh setting? ps: I tried ‘z2pack.fp.kpoint.vasp(5)’ , the message shows the kpt can not be int. 3. Is there a more general example for 2D system, for example Graphene. Thank you for the kind help! Jiaduo Zhu

2 1

Wilson loop?
by Young-Joon Song 24 Mar '17

24 Mar '17

Dear developers, Hello. I have learned about z2pack to calculate Z2 invariants and Chern number. Unfortunately, I mainly use Wien2k code. Is there any plan to implement fp-wien2k on z2pack? Anyway, I make a system using tbmodels with 'wannier90_hr.dat' file. ( This file is from wien2wannier and Wannier90) model = tbmodels.Model.from_hr_file('wannier90_hr.dat') system = z2pack.tb.System(model, bands=6) Is it possible to calculate Wilson loop in this method? If so, can I use kpoints I made? This is because I want to calculate Wilson loop and mirror Chern numbers using kpoints along a line on a mirror plane of BZ. Any comments will be very helpful for me. Thanks in advance.

2 1

Calculate Chern number with an odd number occupied bands in a system
by xiangru kong 07 Mar '17

07 Mar '17

Dear Dominik, Could Z2pack directly calculate the Chern number with first principle codes? I have considered a system with odd number occupied bands (with SOC considered), I set the related parameters the similiar way as the Z2 calculation. surface=lambda s, t: [ s, t, 0] > z2pack.invariant.chern(result_0) and num_wann=num_bands= the number of occupied bands (odd) The error happens in wannier90.wout > > Error: For spinor WF num_wann ust be even Maybe the intrinsic physic in the Chern number I have not known. Thanks Xiangru

2 1

About the mirror chern number
by YU, Hulei 06 Mar '17

06 Mar '17

Dear professor, I am a beginner of Z2Pack. The software could calculate the chern number for TIs conveniently. I would like to know that whether Z2Pack could be used or revised to calculate the Mirror chern number (for *topological crystalline insulator*s). Thanks. Regards Hulei YU Mechanics and Materials Department of Mechanical Engineering #29, COB LG-111, The University of Hong Kong, Pokfulam Road, Hong Kong Email: yuhulei(a)hku.hk or killayhl(a)163.com

2 1

import z2pack error
by Wei Li 03 Mar '17

03 Mar '17

Dear Z2pack team, I have complied Wannier90 1.2 on top of VASP, and then I downloaded and installed z2pack like below: (py35) [verali@farber input]$ python Python 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul 2 2016, 17:53:06) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import z2pack >>> z2pack.__version__ '2.0.3' >>> I think this means I have successfully installed z2pack, right? But when I run run.py script, it had the error: File "run.py", line 14, in <module> Traceback (most recent call last): File "run.py", line 14, in <module> import z2pack ImportError: No module named z2pack Traceback (most recent call last): File "run.py", line 14, in <module> Below is my job file: vpkg_require intel/2015.3.187 vpkg_require openmpi/1.8.5 #$ -pe mpi 40 #$ -l m_mem_free=3G #$ -l h_cpu=09:00:00 ##$ -l exclusive=1 MY_EXE="/home/work/mtg/users/bin/vasp_ncl" MY_EXE_ARGS=() # # Uncomment to enable lots of additional information as OpenMPI executes # your job: # #SHOW_MPI_DEBUGGING=YES ## ## You should NOT need to change anything after this comment. ## OPENMPI_FLAGS="--display-map --mca btl ^openib --mca oob_tcp_if_exclude lo,ib0 --mca btl_tcp_if_exclude lo,ib0" if [ "${WANT_CPU_AFFINITY:-NO}" = "YES" ]; then OPENMPI_FLAGS="${OPENMPI_FLAGS} --bind-to core" fi if [ "${WANT_NPROC:-0}" -gt 0 ]; then OPENMPI_FLAGS="${OPENMPI_FLAGS} --np ${WANT_NPROC} --map-by node" fi if [ "${SHOW_MPI_DEBUGGING:-NO}" = "YES" ]; then OPENMPI_FLAGS="${OPENMPI_FLAGS} --debug-devel --debug-daemons --display-devel-map --display-devel-allocation --mca mca_verbose 1 --mca coll_base_verbose 1 --mca ras_base_verbose 1 --mca ras_gridengine_debug 1 --mca ras_gridengine_verbose 1 --mca btl_base_verbose 1 --mca mtl_base_verbose 1 --mca plm_base_verbose 1 --mca pls_rsh_debug 1" if [ "${WANT_CPU_AFFINITY:-NO}" = "YES" ]; then OPENMPI_FLAGS="${OPENMPI_FLAGS} --report-bindings" fi fi echo "GridEngine parameters:" echo " mpirun = "`which mpirun` echo " nhosts = $NHOSTS” echo " nproc = $NSLOTS" echo " executable = $MY_EXE" echo " MPI flags = $OPENMPI_FLAGS" echo "-- begin OPENMPI run -- on " mpirun ${OPENMPI_FLAGS} python run.py echo "-- end OPENMPI run -- on “ Pls help to advise how can I solve this problem. Thanks in advance. Wei Li Ph.D student University of Delaware

2 15

About calculations
by Sukhwinder Singh 09 Feb '17

09 Feb '17

Good morning I am Sukhwinder Singh pursuing research at panjab university Chandigarh. I works on dft calculation by using Quantum espresso.I want to calculate topological behavior . I want to know how it's check.

2 1

materials with very small band gap
by xiangru kong 07 Feb '17

07 Feb '17

Hi, Dominik, How to set the parameters properly to calculate the topological invariant of a system with a small band gap? The band gap is very tiny which is similar to the Silicene (a 2D QSH insulators with tiny band gap). Now I have set the parameters (to increase the num_lines) below: result_0 = z2pack.surface.run( > > system=system, > > surface=lambda s, t: [ s / 2, t, 0], > > num_lines = 201, > > move_tol = 0.3, > > min_neighbour_dist=0.0005, > > save_file = './results/res_0.p', > > load=True > > ) > > > It seems that the gap checked is always unsuccessful. > +----------------------------------------------------------------------+ | ================== | | CONVERGENCE REPORT | | ================== | | | | Line Convergence | | ================ | | | | PosCheck | | -------- | | PASSED: 337 of 337 | | | | Surface Convergence | | =================== | | | | GapCheck | | -------- | | PASSED: 336 of 336 | | | | MoveCheck | | --------- | | PASSED: 335 of 336 | | FAILED: 1 of 336 Thanks, Xiangru Kong

1 0

help with z2pack installtion
by 张顺洪(Shunhong Zhang) 16 Jan '17

16 Jan '17

Dear z2pack developers, I am writing to seek possible help with the installation of z2pack, I installed it via pip but when I tried importing it in python3, it returns Python 3.5.2 (default, Nov 17 2016, 17:05:23) [GCC 5.4.0 20160609] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import z2pack Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python3.5/dist-packages/z2pack/__init__.py", line 16, in <module> from . import line File "/usr/local/lib/python3.5/dist-packages/z2pack/line/__init__.py", line 13, in <module> from ._data import WccLineData, EigenstateLineData File "/usr/local/lib/python3.5/dist-packages/z2pack/line/_data.py", line 12, in <module> from fsc.export import export ImportError: No module named 'fsc' could you help me identify what is wrong with my installation? thank you very much in advance! Best regards Shunhong -- ------------------------------------------------ Shunhong Zhang Ph.D. (Advanced Materials and Mechanics) Postdoctoral Research Associate Institute for Advanced Study,Tsinghua University -------------------------------------------------

2 1

Troubles calculating Z2 (graphene)
by Jimena Olmos Asar 06 Dec '16

06 Dec '16

Good morning, I am trying to learn how to run the Z2Pack, since it would be really useful for my research project. After some trials, I could get the expected results for two examples you offer: Bi and Bi2Se3. Now I would like to test some known system, like graphene, to check if what I'm doing is correct. Well, it may not be the case, since I can't get Z2=1. Would you, please, give me a hint? I attach the "run.py" file, scf and wannier90 inputs. I also add the pseudopotential (it was generated using the code by Andrea del Corso, within the QE package). Thanks in advance, Jimena Olmos Asar

3 6

KPOINTS file using VASP for Z2pack.fp.system
by Wei Li 02 Nov '16

02 Nov '16

Dear z2pack team, I am a Ph.D student in University of Delaware, and I am studying to do z2 invariants calculation using z2pack. When I creat z2pack.fp.system, I feel confused about the input files. The tutorial shows that the KPOINTS file used in the NSCF run should not be in input files, but when I read run.py, there shows the kpt_path=“KPOINTS” . Do I need to include the KPOINTS file? Can you can me to check if I created the z2pack.fp.system properly as following: z2pack.fp.System file: CONTCAR INCAR KPOINTS PCDAT REPORT WAVECAR DOSCAR input kpts.py POSCAR run.py XDATCAR EIGENVAL jobpython OSZICAR POTCAR vasprun.xml z2pack.fp.kpts.vasp IBZKPT jobz2pack OUTCAR PROCAR wannier90.win input file: CHGCAR DOSCAR INCAR POSCAR POTCAR run.py wannier90.win KPOINTS file: z2pack.fp.kpts.vasp Is that ok? Regards Wei Li

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