Z2Pack

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52 discussions

Issue with wannier90 overlap materices
by Farhat Tasnim 10 Aug '24

10 Aug '24

Hello, I am trying to run z2pack with first principle codes. I generated .win, .mmn files using VASP 6.1 . But when I run the code, after completing the vasp non-collinear step , python returns value error. I have attached a screenshot here. I tried both the files shared on github and those belonging to my research. Even I used the .mmn file that is provided in wannier90 exaples files. In all cases , the same error arises. How to fix it?? Please not that, I am beginner in wannier90 and fixing this problem is quite difficult for me Sincerely, Tasnim

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query
by Ipsita Mandal 12 Jun '24

12 Jun '24

Can we use z2pack for non-Hermitian Hamiltonians? -- Thanking you, Yours Sincerely, Ipsita Mandal

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Regarding the value of Z2-inavriant
by Rameswar Bhattacharjee 06 Dec '23

06 Dec '23

Dear All, I am writing to get some suggestions on computing the value of Z2 of a 1D organic polymer. I am getting the value 0.0 running the program with Quantum Espresso (7.2) and Wannier90. The last two lines are as below: ----------------------------------------------- Z2 topological invariant at kx = 0: 0 Z2 topological invariant at kx = 0.5: 0 ------------------------------------------- I would like to give some information about the QE set up. for thecaluation I am using PBE with ultrasoft pseudopotential. The k point mesh is 12*1*1. The ibrave=0 and the cell_parameters are given in angstroms at the end. Please let me know if you want to know any additional details. The problem is I was expecting the value of Z2=1.0 for this system which was reported earlier. Therefore, my question is if there are any options to rerun the calculation with different parameters which can alter the Z2 value to 1.0 from 0.0. Any suggestions would be highly appreciated. thanks Rameswar -- Rameswar Bhattacharjee Postdoctoral Scholar Georgetown University Washington, DC 20057

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Difficulty Starting Z2-Pack Code for Topological Invariants Calculation
by Rameswar Bhattacharjee 20 Nov '23

20 Nov '23

Hi Everyone I recently set up the Z2-Pack code and also installed Wannier90 on my system. I've been eager to utilize this code alongside Quantum Espresso to compute topological invariants for several systems. However, I've encountered a stumbling block while attempting to initiate the code. An error keeps popping up, indicating a missing '.xml' file from the Quantum Espresso self-consistent field (SCF) calculation. Here's the error message I'm facing: ----------------------------------------------------------- Traceback (most recent call last): File "/home/rb1820/Aromatic-Quininoid/From-Nov14/Poly-Pentyne/qeirreps/equilibrium/For-Z2/BAnd-forZ2/run.py", line 39, in <module> cell = ET.parse('scf/bi.save/data-file.xml').find('CELL').find('DIRECT_LATTICE_VECTORS') File "/home/share/apps/python/anaconda3-3.9/lib/python3.9/xml/etree/ElementTree.py", line 1229, in parse e tree.parse(source, parser) File "/home/share/apps/python/anaconda3-3.9/lib/python3.9/xml/etree/ElementTree.py", line 569, in parse source = open(source, "rb") FileNotFoundError: [Errno 2] No such file or directory: 'scf/bi.save/data-file.xml' ------------------ I've generated four input files (bi.scf.in, bi.nscf.in, bi.pw2wan.in) and placed them in the "input" folder within my working directory. Additionally, the directory contains the 'run.py' code, which I downloaded from GitHub and made modifications to as per the instructions provided. My question pertains to the necessity of running Quantum Espresso separately. According to the instructions, I understood that by providing the paths for Quantum Espresso and Wannier, 'run.py' (attached) should handle all the calculations. Your expertise and guidance would be immensely valuable in resolving this issue. Any suggestions or steps to ensure the seamless execution of the Z2-Pack code would be greatly appreciated. Thank you for your time and assistance. Looking forward to your advice. Thanks Rameswar -- Rameswar Bhattacharjee Postdoctoral Scholar Georgetown University Washington, DC 20057

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Z2Pack Chern Number Example
by Warnock, Michael 18 Jul '23

18 Jul '23

Hi, I'm looking to perform numerical computations for topological materials, including computations involving the Chern number. So, I came across Z2Pack and it seemed intuitive enough for me to use. However, as I've been going through examples and changing parameters/trying to replicate results from the literature, I find myself a little confused about the Haldane model example. I suspect it's some confusion with defining the reciprocal lattice. In particular, in the Z2Pack example reads in a lattice of k-values, then makes arrays for the nearest neighbor and next nearest neighbor k_a and k_b values, then makes those directly the arguments of cosines and sines to determine the Hamiltonian. However, a lot of the literature simplifies the sums of those cosines and sines, where I am performing those calculations to ensure I understand. However, if I directly put in that Hamiltonian with the simplified expressions, (for example assuming k=(kx,ky) and a vector from the honeycomb lattice being (sqrt(3)/2, 1/2), then inner(k,a) = sqrt(3)/2*kx + 1/2*ky), I am unable to get the Chern number to be correct when taking the lattice of k-values that is the argument of the Hamiltonian in Z2Pack. So, where are the k_a and k_b values coming from? Any help would be much appreciated. Thank you, Michael Warnock

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Z2 invariant calculation
by Parrydeep Kaur 24 Mar '22

24 Mar '22

Dear Dominik Gresch, Greetings of the Day!! I am interested in calculating the topological invariant Z2 for a 2D material using the Z2 pack. I have already run the scf, nscf calculations using first principles code Quantum Espresso and further, ran calculations using pw2wan.in and .win files in Wannier90 code. So, I have output files .eig and .mmn. I tried using and editing the code given at " https://z2pack.greschd.ch/en/latest/examples/fp/espresso.html". I dont want to run z2cmd mentioned in line " system = z2pack.fp.System( input_files=input_files, kpt_fct=[z2pack.fp.kpoint.qe, z2pack.fp.kpoint.wannier90], kpt_path=["bi.nscf.in", "bi.win"], command=z2cmd, executable='/bin/bash', mmn_path='bi.mmn')" Instead, I want to use the output files from wannier90 and directly, use them to calculate WCC and topological invariants. Can you please guide and help me out in editing the code accordingly. Waiting for your reply. Thanking you, Parrydeep Kaur Sachdeva Research Scholar Institute of Nano Science and Technology Mohali, India

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Error in the calculation of Z2 invariant of Kane-Mele Model
by SAYAN MONDAL 18 Sep '21

18 Sep '21

Dear Developer, I am trying to get the phase diagram of the Kane-Mele model as described in Fig. 1 of (https://doi.org/10.1103/PhysRevLett.95.146802). The Z2 invariant is 1 inside the curve while it vanishes outside. So I tried to get the Z2 invariant for several values of lambda_R and lambda_v. The code is giving correct results for some values of lambda_R and lambda_v, but for some other values it is showing some errors as follows: WARNING: Iterator stopped before the calculation could converge. WARNING: Iterator stopped before the calculation could converge. WARNING: 'min_neighbour_dist' reached: cannot add line at t = 0.6562500000000001 WARNING: Iterator stopped before the calculation could converge. WARNING: Iterator stopped before the calculation could converge. WARNING: 'min_neighbour_dist' reached: cannot add line at t = 0.6562500000000001 WARNING: Iterator stopped before the calculation could converge. WARNING: Iterator stopped before the calculation could converge. WARNING: 'min_neighbour_dist' reached: cannot add line at t = 0.6562500000000001 My code is attached below: ************************************* import logging import z2pack import numpy as np from numpy import cos, sin, kron, sqrt import matplotlib.pyplot as plt logging.getLogger('z2pack').setLevel(logging.WARNING) # defining pauli matrices identity = np.identity(2, dtype=complex) pauli_x = np.array([[0, 1], [1, 0]], dtype=complex) pauli_y = np.array([[0, -1j], [1j, 0]], dtype=complex) pauli_z = np.array([[1, 0], [0, -1]], dtype=complex) def get_kane_mele_hamiltonian(t, lambda_v, lambda_R, lambda_SO): def inner(k): k = np.array(k) * 2 * np.pi kx, ky = k # change to reduced coordinates x = (kx - ky) / 2 y = (kx + ky) / 2 return ( t * (1 + 2 * cos(x) * cos(y)) * kron(pauli_x, identity) + lambda_v * kron(pauli_z, identity) + lambda_R * (1 - cos(x) * cos(y)) * kron(pauli_y, pauli_x) + -sqrt(3) * lambda_R * sin(x) * sin(y) * kron(pauli_y, pauli_y) + 2 * t * cos(x) * sin(y) * kron(pauli_y, identity) + lambda_SO * (2 * sin(2 * x) - 4 * sin(x) * cos(y)) * kron(pauli_z, pauli_z) + lambda_R * cos(x) * sin(y) * kron(pauli_x, pauli_x) + -sqrt(3) * lambda_R * sin(x) * cos(y) * kron(pauli_x, pauli_y) ) return inner if __name__ == '__main__': arr = [] lambda_R_list = np.linspace(0, 0.31, 20) lambda_v_list = np.linspace(0, 0.24, 20) for lR in lambda_R_list: for lv in lambda_v_list: system = z2pack.hm.System( get_kane_mele_hamiltonian( t=1, lambda_v = lv, lambda_R=lR, lambda_SO=0.06 ), dim=2, check_periodic=True ) res = z2pack.surface.run(system=system, surface=lambda s, t: [s / 2, t]) # print('Z2 invariant: {}'.format(z2pack.invariant.z2(res))) val = z2pack.invariant.z2(res) arr.append([lR, lv, val]) arr = np.asarray(arr) np.savetxt('pd.txt', arr) print(arr) # z2pack.plot.wcc(res, axis=ax) # ax.set_xticks([0, 1]) # ax.set_xticklabels(['0', '0.5']) # ax.set_xlabel(r'$k_y$') # ax.set_yticks([0, 1]) # ax.set_ylabel(r'$\bar{y}$', rotation='horizontal') # plt.savefig('plot.pdf', bbox_inches='tight') ************************************************** Is there any way to correct those errors? I shall look forward to your kind cooperation. Thank you Best Regards, Sayan Mondal, Research Scholar, Dept. of Physics, Roll No. - 186121022, E-mail: mondal18(a)iitg.ac.in Indian Institute of Technology Guwahati Guwahati - 781039

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Running Z2 pack with Quantum espresso
by Rijan Karkee 03 Aug '21

03 Aug '21

Hello Developer, I have quantum espresso v 6.1 and wannier90 v3.1.0 in my system. I am new to this and I could not run the examples file for Bi although I copied everything. I need to compute later in my system of MoS2 and I have no clue in setting the system. I went through the website and tried my best to learn. I would say I am a beginner in Python, I can see some basics things going there. When I copied the github example and tried running it in my system, I got the following. 1) Folders were created namely "build', "plots", "results:, and "scf" 2) The scf calculation ran successfully 3) inside build folder, there were two log file, pw.log seems fine. But pw2wan.log has following error: [proxy:0:0@mrcd103.cluster] HYDU_sock_write (utils/sock/sock.c:286): write error (Broken pipe) [proxy:0:0@mrcd103.cluster] HYD_pmcd_pmip_control_cmd_cb (pm/pmiserv/pmip_cb.c:958): unable to write to downstream stdin [proxy:0:0@mrcd103.cluster] HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status [proxy:0:0@mrcd103.cluster] main (pm/pmiserv/pmip.c:206): demux engine error waiting for event [mpiexec(a)mrcd103.cluster] control_cb (pm/pmiserv/pmiserv_cb.c:200): assert (!closed) failed [mpiexec(a)mrcd103.cluster] HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status [mpiexec(a)mrcd103.cluster] HYD_pmci_wait_for_completion (pm/pmiserv/pmiserv_pmci.c:198): error waiting for event [mpiexec(a)mrcd103.cluster] main (ui/mpich/mpiexec.c:344): process manager error waiting for completion 4) There is a file called bi.werr that has this information : Wannier90: Execution started on 27Jul2021 at 09:57:16 Exiting....... Input parameter nnkpts_block is allowed only if postproc_setup = .true. I am also new to Wannier90, but then I managed to run a separate calculation for Wannier90 on MoS2. It was working properly. But the example for bi.win looks totally different for what I have. Where can I find what to include and what not to include in input.win file? Can anyone please help me resolve my issues? Is there any simpler step by step tutorial for beginners like me? Thank you Best Rijan Karkee

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database of kpoints and corresponding hamiltonians
by Palmer, Daniel 23 Jul '21

23 Jul '21

Hello, I have files containing k points and their corresponding hamiltonians from extended huckel calculations. Is there any way I can create a z2pack.hm.System object using this data? I know I can create a Hamiltonian function that takes in a specific k point and returns the associated Hamiltonian at the k point, but I can't figure out how to force z2pack to generate the k points I have stored in the file. I have attached what I have so far, (see line 124 for code that creates system, and line 94 for Hamiltonian function). I parse data from mp_47.out and store the kpoints, and Hamiltonian in a [n,3] numpy array and [n,16,16] numpy array, respectively, where n is the number of kpoints. Best, Dan

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Error in running Z2pack code
by Vineet Kumar Sharma 22 Jun '21

22 Jun '21

Respected Sir, This is Vineet Kumar Sharma, a research scholar from IIT Hyderabad. I am a beginner to this code. I followed the steps to modify the run.py program given for Bi. While executing this program, I am getting this error. +----------------------------------------------------------------------+ |=================== | |SURFACE CALCULATION | |=================== | |starting at 2021-06-22 12:46:31,818 | |running Z2Pack version 2.2.0 | | | |gap_tol: 0.3 | |init_result: None | |iterator: range(8, 27, 2) | |load: True | |load_quiet: True | |min_neighbour_dist: 0.01 | |move_tol: 0.3 | |num_lines: 11 | |pos_tol: 0.01 | |save_file: ./results/res_0.p | |serializer: auto | |surface: <function <lambda> at 0x153c71281268> | |system: <z2pack.fp._first_prin<...>ject at 0x153c7b232b00>| +----------------------------------------------------------------------+ INFO: Adding lines required by 'num_lines'. INFO: Adding line at t = 0.0 INFO: Calculating line for N = 8 /bin/sh: 1: Syntax error: Bad fd number Traceback (most recent call last): File "/home/kanchana/.local/lib/python3.6/site-packages/z2pack/fp/_read_mmn.py", line 16, in get_m with open(mmn_file, "r") as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/kanchana/Soft/Z2Pack-dev-current/examples/fp/vasp/ Bi/build/wannier90.mmn' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "run.py", line 37, in <module> load=True File "/home/kanchana/.local/lib/python3.6/site-packages/decorator.py", line 232, in fun return caller(func, *(extras + args), **kw) File "/home/kanchana/.local/lib/python3.6/site-packages/z2pack/_run_utils.py", line 21, in inner result = fct(**kwargs) File "/home/kanchana/.local/lib/python3.6/site-packages/z2pack/surface/_run.py", line 131, in run_surface serializer=serializer File "/usr/lib/python3.6/contextlib.py", line 52, in inner return func(*args, **kwds) File "/home/kanchana/.local/lib/python3.6/site-packages/z2pack/surface/_run.py", line 269, in _run_surface_impl result = add_line(t) File "/home/kanchana/.local/lib/python3.6/site-packages/z2pack/surface/_run.py", line 207, in add_line data.add_line(t, get_line(t)) File "/home/kanchana/.local/lib/python3.6/site-packages/z2pack/surface/_run.py", line 171, in get_line init_result=init_line_result File "/home/kanchana/.local/lib/python3.6/site-packages/z2pack/line/_run.py", line 193, in _run_line_impl for k in np.linspace(0., 1., run_options['num_steps']) File "/home/kanchana/.local/lib/python3.6/site-packages/ z2pack/fp/_first_principles.py", line 145, in get_mmn overlap_matrices = mmn.get_m(self._mmn_path) File "/home/kanchana/.local/lib/python3.6/site-packages/z2pack/fp/_read_mmn.py", line 58, in get_m raise type(err)((msg)) from err FileNotFoundError: [Errno 2] No such file or directory: '/home/kanchana/Soft/Z2Pack-dev-current/examples/fp/vasp/Bi/build/wannier90.mmn'. Check that the path of the .mmn file is correct (mmn_path input variable). If that is the case, an error occurred during the call to the first-principles code and Wannier90. Check the corresponding log/error files. Please help me out to fix this error. Thanks & Regards, Vineet Kumar Sharma Research Scholar IIT Hyderabad M No. - 9133708132 -- Disclaimer:- This footer text is to convey that this email is sent by one of the users of IITH. So, do not mark it as SPAM.

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