Dear all,

I'm a new user of BandUp and Quantum Espresso(V6.0). When I'm trying to run step4, I receive this error:

ERROR (read_qe_evc_file): Could not determine the number of plane-waves for the current Kpt.
I tried to find the reason by looking at "read_qe_wavefunctions_mod.f90" but because of my poor coding background, I just couldn't understand it.
Could anyone tell me how to fix this? I have attached my input files for your reference.
Thank you!

GeInTe_scf_in.txt
KPOINTS_prim_cell.txt
prim_cell_lattice.txt
supercell_lattice.txt
GeInTe_bands_in.txt

Dear BandUP developers,

I am getting one error while compiling ./build in our cluster as follows:

ifort: error #10236: File not found: '/home/gargeeb/BandUP/bandup-master/src/external/spglib-1.5.2/src/.libs/libsymspg.a'
make: *** [get_SCKPTS_pre_BandUP.x] Error 1

Please suggest me to solve this issue.

Best regards
Gargee

There is a big issue related to work with never versions of Quantum Espresso.
As of version 6.4., QE does not support old file format any more (former -D_OLDXML option), so, right now, we are forced to stick with older versions of QE to use with BandUP.

Josip Jakovac

Hi!

Dose bandup support extracting the carrier effective mass near the band edge from the 'unfolded-symmetry-average.dat'?

Looking at your code, here and here it seems spin polarized cases are not implemented, (else this would segfault: bandup/src/external/espresso-5.1_modules_for_BandUP/Modules/qexml.f90 line 4026,ik_eff would lead to an overflow, going beyond number of kpoints, meaning this was considered but not implemented), what is needed to introduce proper support for spin polarized cases?

Hi, could anyone tell me how to make it works with Quantum Espresso 6.5 or beyond, please?

I would like to report this issue faced when running ./build, the installation process works normally until it gets to the step of spglib-1.5.2/, the script seems to be complaining about the C compiler and will throw an error as you can see in the following:

cd spglib-1.5.2;
./configure FC=gfortran CC=gcc CFLAGS=-fopenmp FCFLAGS=-fopenmp;
cd /Users/Downloads/Crystallography/bandup/src/external
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /opt/local/bin/gmkdir -p
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in /Users/Downloads/Crystallography/bandup/src/external/spglib-1.5.2': configure: error: C compiler cannot create executables See config.log' for more details
cd spglib-1.5.2;
/Library/Developer/CommandLineTools/usr/bin/make -j --max-load 2.5;
cd /Users/Downloads/Crystallography/bandup/src/external
make[1]: *** No targets specified and no makefile found. Stop.
gfortran -std=gnu -pedantic -fopenmp -O2 -w -I/Users/Downloads/Crystallography/bandup/src/external/espresso-5.1_modules_for_BandUP/Modules -I/Users/Downloads/Crystallography/bandup/src/external/espresso-5.1_modules_for_BandUP/iotk/src main_get_SCKPTS_pre_BandUP.o cla.o kinds.o constants_and_types_mod.o cla_wrappers_mod.o spglib_f08.o lists_and_seqs_mod.o time_mod.o units_mod.o crystals_mod.o math_mod.o symmetry_mod.o band_unfolding_routines_mod.o general_io_mod.o read_wavecar_mod.o read_vasp_files_mod.o read_abinit_wavefunctions_mod.o read_qe_wavefunctions_mod.o write_vasp_files_mod.o strings_mod.o io_routines_mod.o /Users/Downloads/Crystallography/bandup/src/external/spglib-1.5.2/src/.libs/libsymspg.a /Users/Downloads/Crystallography/bandup/src/external/espresso-5.1_modules_for_BandUP/Modules/libqemod.a /Users/Downloads/Crystallography/bandup/src/external/espresso-5.1_modules_for_BandUP/flib/ptools.a /Users/Downloads/Crystallography/bandup/src/external/espresso-5.1_modules_for_BandUP/flib/flib.a /Users/Downloads/Crystallography/bandup/src/external/espresso-5.1_modules_for_BandUP/clib/clib.a /Users/Downloads/Crystallography/bandup/src/external/espresso-5.1_modules_for_BandUP/iotk/src/libiotk.a -o get_SCKPTS_pre_BandUP.x
ld: file not found: /Users/Downloads/Crystallography/bandup/src/external/spglib-1.5.2/src/.libs/libsymspg.a
collect2: error: ld returned 1 exit status
make: *** [get_SCKPTS_pre_BandUP.x] Error 1

Dear Bandup authors,

Have you tried making a pypi package out of bandup? Is there a reason why it would not work out?

That means, converting build into setup.py

It would make installation that much simpler!

Here is a relevant example:
https://stackoverflow.com/questions/55352409/python-setuptools-compile-fortran-code-and-make-an-entry-points

Best regards,

• Simppa -

We have tried compiling this program with two different computers, one was a fresh install of python, python3, pip, numpy, scipy, matplotlib, six, etc.

We are getting the same error for both computers:
$ ./build Traceback (most recent call last): File "./build", line 26, in <module> from bandupy.files import mkdir File "/home/lom/Documents/bandup-master/src/python_interface/bandupy/files.py", line 23, in <module> from scipy.constants import physical_constants ImportError: No module named scipy.constants

We have tried to change the code to things like "import scipy" with same error. It does not seem to recognize scipy. No internet searches have helped and we have puzzled over it for a long time without a clue. Any help would be appreciated. Thanks!

Dear BandUP Developers,

I am getting one error while generating SC k-path. Please help me to solve this problem. I have attached here the inputs.

step_2_get_kpts_to_be_used_in_the_SC_band_struc_calcs.zip

Thanks & regards
Gargee

**===========================================================================
BandUP: Band Unfolding code for Plane-wave based calculations
v3.0.0-beta.6-9-gbd3ff1f, 2021-04-13 18:34:21 +0200
From Git branch: "master"
Compiled using Intel Fortran (ifort) V1910 on Thu Nov 04 10:39:07 2021

Copyright (C) 2013-2017 Paulo V. C. Medeiros

                    Computational Physics Division                     
                    Department of Physics, Chemistry and Biology - IFM 
                    Link񯨮g University                               
                    Sweden                                             
                                                                       
                    Current address:                                   
                    University of Cambridge                            
                    Theory of Condensed Matter (TCM) Group             
                    Department of Physics                              
                    Cavendish Laboratory                               
                    Cambridge, UK                                      
                    Email: [email protected]                             

Please visit www.ifm.liu.se/theomod/compphys/band-unfolding

           Pre-processing utility "get_SCKPTS_pre_BandUP"

Getting the SC-KPTS you'll need for your plane-wave calc. <<<

Checking if you are working with the smallest possible SC:
* OK!

Checking if working with the smallest possible ref. unit cell:
* OK!
Traceback (most recent call last):
File "/home/gargeeb/BandUP/bandup/bandup", line 73, in
run_requested_task(args)
File "/home/gargeeb/BandUP/bandup/src/python_interface/bandupy/runners.py", line 73, in run_requested_task
run_pre_bandup_tool(args)
File "/home/gargeeb/BandUP/bandup/src/python_interface/bandupy/runners.py", line 53, in run_pre_bandup_tool
for line in iter(bandup_pre_unf_run.stdout.readline, ''):
File "/comm/swstack/core/anaconda3/2021.05/lib/python3.8/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xcd in position 1556: invalid continuation byte**

Running bandup kpts under Python3, I get the following error:

Traceback (most recent call last):
  File "/home/e/bjm42/bin/bandup", line 73, in <module>
    run_requested_task(args)
  File "/home/e/bjm42/source/bandup/src/python_interface/bandupy/runners.py", line 73, in run_requested_task
    run_pre_bandup_tool(args)
  File "/home/e/bjm42/source/bandup/src/python_interface/bandupy/runners.py", line 54, in run_pre_bandup_tool
    sys.stdout.write(line)
TypeError: write() argument must be str, not bytes

This looks to me like Python 3 being stricter about byte vs. string IO streams, but could be something entirely different.

Dear Dr. Tsirkin,
Thank you for building the amazing bandup package!

When the vmax is less than 1, I noticed that the color bar doesn't show the upper range like attached. Is there a setting for it to show fraction like 0.4? I tried adding: --cb_label --round_cb 2 --disable_auto_round_vmin_and_vmax

Can I make the code display the greek letter gamma? I notice the issue only when I have discontinuities like U,K.
I tried // Gamma too. Thank you so much!

Hi guys, great tool!

Unfortunately it did not work "out of the box" (might be related to my python 2.7 on ubuntu), I had to add

shell=True

on line 36 in version.py

def get_latest_git_tag():
    tag = None
    get_tag_run = Popen(['git', 'describe', '--tags', '--dirty'],
                           stdout=PIPE, stderr=PIPE, shell=True)
    stdout, stderr = get_tag_run.communicate()
    if(not stderr.strip()):
        tag = stdout.strip()
    return tag

otherwise it would throw

Traceback (most recent call last):
  File "/home/chris/Downloads/bandup-master/bandup", line 71, in <module>
    parser = BandUpPythonArgumentParser()
  File "/home/chris/Downloads/bandup-master/src/python_interface/bandupy/argparse_wrapper.py", line 643, in __init__
    version='%(prog)s {version}'.format(version=__version__()))
  File "/home/chris/Downloads/bandup-master/src/python_interface/bandupy/version.py", line 43, in get_package_version
    pv = get_latest_git_tag()
  File "/home/chris/Downloads/bandup-master/src/python_interface/bandupy/version.py", line 36, in get_latest_git_tag
    stdout=PIPE, stderr=PIPE)
  File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Best,
Chris

Hello,
Thank you for such wonderful code. I have compiled all the steps for plotting bands structure of Si within the tutorial directory of band-up. After executing the forth step i found a bands structure of Si with a color scale plotting in Matplotlib. I do not understand the color map. what the color map signifies? please clear my confusion. Also I am running the code with QE version 6.1. For higher version of QE like 6.7, I found error in the forth step of band-up Si tutorial case. why this is so? Is it not consistent with higher version of QE?

Thanking you,
Sourav

ifort is returning an error stating that
File not found: '/bandup-master/src/external/spglib-1.5.2/src/.libs/libsymspg.a'
Sure enough, the file isn't there, and neither is the parent directory .libs

Dear All,
I have just started using Band Up code to unfold bandstructures. I have tried to unfold bandstructure of pristine supercell. For that i have supplied POSCARs of primitive cell and super cell and got the desired result. But in case of defects, where we generally make supercells, how can we define primitive cell? I'm a bit confused here. In case I take pristine primitive cell then the code gives error that they are not commensurate.
Any help would be highly appreciated.
Thanks and Regards

Hi all,
When I run a projection for d orbitals I get as information :
* OrbitalProjector: dxy+dyz+dz2+dxz
is dx2-y2 not included?
when I specify dx2 only i get
Invalid choice of orbital: "dx2"

Hi,
I am using VASP for my calculations. I did step1,step2, and step3 but when I typed bandup where I need to unfold the bands, it does not create an energy.info automatically. What could be the reason for it?
Thank you.

Dear developer,
I would like to plot without blue color background in the final plot. I got nice final plot which I attached here(221 unit cell of WS2 monolayer), but I could not remove the blue color background. Any help is appreciate.

Thank you

Hello I am a new user to qe. Whenever I try to execute the command it says the following:
./build
Traceback (most recent call last):
File "./build", line 26, in
from bandupy.files import mkdir
File "/home/satabdee/bandup-master-main/src/python_interface/bandupy/files.py", line 23, in
from scipy.constants import physical_constants
ImportError: No module named scipy.constants

please help

Hello;
i compiled the last version of bandup. i m using python 2.7 and as default and QE 6.4. when following the tutorial example 2 ( bulk Si) and in the step 4 i have an error:

You have compiled BandUP without support for QE!
and
unfolded_EBS_symmetry-averaged.dat does not exist or is not accessible.

i tried to solve the problem without success.
any suggestion!!!?

Hi all,
Does orbital projection can be gotten by BandUp code when spin-orbital coupling(SOC) is turned on? I can get the orbital projection without SOC. However, when SOC is turned on, I didn't get the right orbital projection. If this feature is implemented, whether any parameter setting is different from without SOC case?
Thanks all of you very much.

Facing this type of error... please provide suggestions.

shuva@shuva:~/bandup-master$ ./build
BandUP will be compiled using gfortran (compiler determined automatically)
sh: 1: make: not found
sh: 1: make: not found

In the post unfolding utility, line 658 of the code 'plot_unfolded_EBS_BandUP.py' is: 'if symb_dict.has_key(input_list[i].upper()):'
However, this 'has_key()' was removed in python3 and it has to be replaced by '__ contains __()'. It solved my problem. This is just a minor issue, I hope this will be helpful.

Hi,

I am trying to do band unfolding of BiSe-NbSe2 misfit structure on NbSe2 hexagonal unit cell. I am using VASP for my calculation. I have already generated the CHGCAR file for the misfit structure (BiSe-NbSe2). I have also done the optimization and band structure calculation NbSe2 primitive cell.

I am getting error while generating the effective band path (supercell band path) for band structure calculation and I got error as:

> ===========================================================================
> 
>                Pre-processing utility "get_SCKPTS_pre_BandUP"
>    >>> Getting the SC-KPTS you'll need for your plane-wave calc. <<<
> 
> 
>  Checking if you are working with the smallest possible SC:
>      * Your SC seems to be a perfect repetition of a smaller PC!
>        > That's OK if you really want it, but using the smallest
>          possible SC will certainly save you some time!
>      * We attempted to find a possible PC associated with it.
>        Please take a look at the file "BandUP_suggestion_of_smaller_SC_based_on_your_input_SC.POSCAR".
> 
>  Checking if working with the smallest possible ref. unit cell:
>      * OK!
>  
>  
> ===========================================================================
>                                      ERROR!!                                                                                                                                                                                                                    
> ===========================================================================
>   The SC and the reference PC that you have chosen are not commensurate!  
>   The choice of the reference PC vectors is very important and can change 
>   a lot the results of unfolding. It is particularly important to always  
>   verify that the SC and the reference PC are commensurate. Otherwise, the
>   calculated spectral weigths will most likely be very small, which will  
>   certainly cause the values of the unfolded delta_Ns to be also small.   
> ===========================================================================
> 
>  
> Traceback (most recent call last):
>   File "/home/au658188/Downloads/bandup-master/bandup", line 73, in <module>
>     run_requested_task(args)
>   File "/home/au658188/Downloads/bandup-master/src/python_interface/bandupy/runners.py", line 73, in run_requested_task
>     run_pre_bandup_tool(args)
>   File "/home/au658188/Downloads/bandup-master/src/python_interface/bandupy/runners.py", line 53, in run_pre_bandup_tool
>     for line in iter(bandup_pre_unf_run.stdout.readline, ''):
>   File "/home/au658188/anaconda3/lib/python3.8/codecs.py", line 322, in decode
>     (result, consumed) = self._buffer_decode(data, self.errors, final)
> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 628: invalid start byte

I am attaching the inputs I have used to generate the SC K-path. Moreover, the suggested POSCAR (supercell) file also seems very different than the one gave as input.
Unfold_on_NbSe2.zip

Please help me to solve this error.

Hi,
I am trying to unfold the band structure of a defect Nb0.8CoSb on its primitive fcc structure NbCoSb.
I am facing few problems while unfolding as follows

1. it is not detecting the symmtery properly as NbCOSb has space group (F-43m) and it is detecting(F-m3m).
2. I am getting the error "Failed to determine GUR" while using flag unfold

Can you help me out?
thanks

Hello I am a new user to qe. Whenever I try to execute the command it says the following:
./build
Traceback (most recent call last):
File "./build", line 26, in
from bandupy.files import mkdir
File "/home/satabdee/bandup-master-main/src/python_interface/bandupy/files.py", line 23, in
from scipy.constants import physical_constants
ImportError: No module named scipy.constants

please help

Your code is very helpful! Ihave a question whether it is supported in SOC calculation in VASP and provides band projection on specific element or orbitals?

Thank you!

Dear all,
Is there a detailed document for writing the inputfiles for BandUP?
The install tar ball only provides the example files in step_2* dir, but no enough comment in it.

Best regards.
Youzhao Lan
China

Hello,
When I try to do a "bandup unfold" calculation (using a .sh script given in examples), it says that cannot find a "data-file.xml" file in .save folder, and, yes, there is none. Most similar is "data-file-schema.xml". What might be the solution of this problem? I tried to rename it to asked file name, but that does not work. I am using quantum espresso 6.2 and the latest version of BandUP, in python 2 environment (switched from python 3, as there are some issues with it).

Screen output data file as an attachment.
unfold_out.txt

Thanks,
Josip

i am currently finishing up installing software on our computing cluster and I need to know what version of QE should I be installing for bandup to work (I can install several since I am using easybuild)

thank you