import z2pack error

Dominik Gresch greschd at phys.ethz.ch
Sun Feb 26 00:19:39 CET 2017


Dear Wei Li,

You can analyze the topological phase of these results with the 
functions given in Z2Pack: 
http://z2pack.ethz.ch/doc/2.0/tutorial_invariants.html

This is much more reliable than trying to estimate it from the plots of 
the result -- indeed, the plots are usually for illustration purposes only.

Best regards,

Dominik


On 24.02.2017 21:22, Wei Li wrote:
> Dear Dominik,
>
> Thanks so much for all of you help. I am comfortably run z2pack now.
>
> I did some tests for semimetal bulk and one single layer and attached 
> are my results.
>
> I am not sure is you are ok to help to analyze what is the topological 
> phases of the attached two results?
>
> I apologise for any inconvenience caused.
>
> Regards
> Wei Li
>
>
>
>
>
>
>
>> On Feb 20, 2017, at 12:00 PM, Dominik Gresch <greschd at phys.ethz.ch 
>> <mailto:greschd at phys.ethz.ch>> wrote:
>>
>> Hi Wei Li,
>>
>> There is clearly something wrong with these results -- there are far 
>> too many Wannier charge centers. This has nothing to do with the 
>> input parameters to Z2Pack. Instead, the input files for VASP or 
>> Wannier90 are generating too many bands. The reason for this might be 
>> that VASP automatically adds more bands when the number of bands 
>> doesn't fit the number of cores on which the calculation is running. 
>> Since Wannier90 has no way of automatically ignoring these, they are 
>> included in the calculation.
>>
>> There are two ways of solving this:
>>
>>     1. Change the number of cores on which you run, such that only 
>> the 15 NBANDS are actually calculated
>>
>>     2. Check the number of bands that is actually used (you should 
>> find this in the VASP output file), and change the upper limit of 
>> "exclude_bands" in wannier90.win
>>
>> Best regards,
>> Dominik
>>
>> On 20.02.2017 17:50, Wei Li wrote:
>>> Hi Dominik,
>>>
>>> Thanks.
>>>
>>> I generated the plot for Bi calculation as attached.  But there are 
>>> very high dense KPOINTS. I thought I change optimize it by set the 
>>> parameter iterator=range as following:
>>>
>>>
>>> result_0 = z2pack.surface.run(
>>>     system=system,
>>>     surface=lambdas, t: [0, s / 2, t],
>>>     iterator=range(10,24,2),
>>>     save_file='./results/res_0.p',
>>>     load=True
>>>
>>> But it generate same result.
>>>
>>> Or do I need to set s limit by pos_tol?
>>>
>>> Regards
>>> Wei Li
>>>
>>>
>>>
>>>
>>>> On Feb 16, 2017, at 5:37 PM, Dominik Gresch <greschd at phys.ethz.ch 
>>>> <mailto:greschd at phys.ethz.ch>> wrote:
>>>>
>>>> Dear Wei Li,
>>>>
>>>> The surface is parametrized as a function of two parameters, as 
>>>> described here: 
>>>> http://z2pack.ethz.ch/doc/2.0/tutorial_surface.html#basic-syntax
>>>>
>>>> For VASP, it is important to note that the surface must be straight 
>>>> in the second parameter (that is, f(t1=const., t2) describes a 
>>>> straight line across the full BZ, parallel to one of the reciprocal 
>>>> axes). This is again due to a limitation in the interface between 
>>>> Wannier90 and VASP, where only automatic mesh generation is possible.
>>>>
>>>> For your second question about the progress of the calculation: To 
>>>> see the progress of your calculation, it is much more helpful to 
>>>> look at the output of Z2Pack itself instead of the build folder or 
>>>> the result file. Z2Pack reports which lines it is calculating, and 
>>>> what the status of the convergence is.
>>>>
>>>> You can improve the performance for example if you find that the 
>>>> iteration in a single line never converges before a specific value, 
>>>> by adjusting the 'iterator' parameter accordingly. The main reason 
>>>> it can sometimes take a long time is because of the adaptive 
>>>> convergence criteria. This is a tradeoff we made on purpose, 
>>>> because it significantly improves the reliability of the results. 
>>>> Of course you can turn them off, but I would strongly advise 
>>>> against this. All in all, performance was not so much the focus in 
>>>> developing Z2Pack as reliability and flexibility in using it for 
>>>> different purposes.
>>>>
>>>> Best regards,
>>>>
>>>> Dominik
>>>>
>>>>
>>>> On 16.02.2017 22:15, Wei Li wrote:
>>>>> Dear Dominik,
>>>>>
>>>>> Thanks, I have complied wannier90 2.1 on top of VASP and I am 
>>>>> doing the test currently.
>>>>>
>>>>> I noticed that z2pack dynamically generate the KPOINTS files for 
>>>>> WCC calculations. Everything runs well except that I am not sure 
>>>>> about parameterizing the
>>>>> surface, which means that when the KPOINTS loop can end. So far my 
>>>>> KPOINTS files reach to like below:
>>>>>
>>>>> Automatic mesh
>>>>> 0   ! number of k-points = 0 ->automatic generation scheme
>>>>> Gamma   ! generate a Gamma centered grid
>>>>> 1 1 17   ! subdivisions
>>>>> 0.0 0.03125 0.0! shift
>>>>>
>>>>>
>>>>> Do I need to set a parameter to end the KPOINTS shifting, or I 
>>>>> just need to waiting for the calculation completed as the 
>>>>> parameters in the tutorial? So far, it realy
>>>>> consumes lots of computation time. Here is my results file 
>>>>> information:
>>>>>
>>>>> [wli9 at br006 Z2]$ ls -artl results/
>>>>> total 1026
>>>>> -rw------- 1 wli9 mr4s90p 75853 Feb 16 16:13 res_0.p
>>>>> drwxr-xr-x 2 wli9 mr4s90p 33280 Feb 16 16:13 .
>>>>> drwxr-xr-x 6 wli9 mr4s90p 33280 Feb 16 16:13 ..
>>>>>
>>>>> Regards
>>>>> Wei Li
>>>>>
>>>>>
>>>>>> On Feb 13, 2017, at 5:44 PM, Dominik Gresch <greschd at phys.ethz.ch 
>>>>>> <mailto:greschd at phys.ethz.ch>> wrote:
>>>>>>
>>>>>> Dear Wei Li,
>>>>>>
>>>>>> The Bi example should run with the supplied input files. However, 
>>>>>> you need to install a modified version of Wannier90, as explained 
>>>>>> in the installation instructions: 
>>>>>> http://z2pack.ethz.ch/doc/2.0/tutorial_installation.html#setting-up-first-principles-codes
>>>>>>
>>>>>> For Wannier90 2.1 or newer this is no longer necessary because we 
>>>>>> added a specific interface to run with Z2Pack, but unfortunately 
>>>>>> VASP only supports Wannier90 version 1.x.
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Dominik Gresch
>>>>>>
>>>>>>
>>>>>> On 13.02.2017 23:40, Wei Li wrote:
>>>>>>> Hi Dominik,
>>>>>>>
>>>>>>> Thanks, it runs well now.
>>>>>>>
>>>>>>> For the given example (Bi) calculation, I need to set up the 
>>>>>>> search_shells number. What’s the value you recommend?
>>>>>>> I have increased to 30 from default value 12, it still can not 
>>>>>>> satisfy the B1 condition:
>>>>>>>
>>>>>>>  Unable to satisfy B1 with any of the first  30 shells
>>>>>>>  Your cell might be very long, or you may have an irregular MP grid
>>>>>>>  Try increasing the parameter search_shells in the win file 
>>>>>>> (default=12)
>>>>>>>
>>>>>>> Or do I need to check other parameters?
>>>>>>>
>>>>>>> Here is my input:
>>>>>>>
>>>>>>> num_wann = 10
>>>>>>> num_bands = 10
>>>>>>> spinors : true
>>>>>>> search_shells=30
>>>>>>> num_iter 0
>>>>>>> exclude_bands 11-15
>>>>>>>
>>>>>>> Regards
>>>>>>> Wei Li
>>>>>>>
>>>>>>>
>>>>>>>> On Feb 11, 2017, at 4:00 PM, Dominik Gresch 
>>>>>>>> <greschd at phys.ethz.ch <mailto:greschd at phys.ethz.ch>> wrote:
>>>>>>>>
>>>>>>>> Dear Wei Li,
>>>>>>>>
>>>>>>>> If everything work correctly, Z2Pack should automatically call 
>>>>>>>> VASP (via the command given) and read the .mmn file after VASP 
>>>>>>>> has generated it. This is because Z2Pack needs to iteratively 
>>>>>>>> change the k-point path with which VASP is called and the 
>>>>>>>> overlap file is calculated.
>>>>>>>>
>>>>>>>> In your case, it seems that you are submitting the VASP run to 
>>>>>>>> some scheduler -- this means the command returns immediately, 
>>>>>>>> before the .mmn file has been generated. As a result, Z2Pack 
>>>>>>>> tries to read the file, but it does not exist yet. You can 
>>>>>>>> solve this problem by submitting instead the Python process 
>>>>>>>> running Z2Pack, and then running VASP within that same job.
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>> Dominik
>>>>>>>>
>>>>>>>>
>>>>>>>> On 11.02.2017 20:40, Wei Li wrote:
>>>>>>>>> Dear Dominik,
>>>>>>>>>
>>>>>>>>> From what I understand, after calling the first principle code 
>>>>>>>>> (in my case, it is VASP), the next step is to
>>>>>>>>> read the .mmn file in the top level of the build file. So I 
>>>>>>>>> give the mmn path like below:
>>>>>>>>>
>>>>>>>>> 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="qsub /home/work/mtg/users/verali/Bi_Z2/Z2/paral.qs"
>>>>>>>>> mmn_path="wannier90.mmn"
>>>>>>>>> )
>>>>>>>>>
>>>>>>>>> But it does not work.
>>>>>>>>>
>>>>>>>>> Could you advise how to read the mmn file?
>>>>>>>>>
>>>>>>>>> Regards
>>>>>>>>> Wei Li
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> On Feb 10, 2017, at 2:59 PM, Wei Li <verali at udel.edu 
>>>>>>>>>> <mailto:verali at udel.edu>> wrote:
>>>>>>>>>>
>>>>>>>>>> Dear Dominik,
>>>>>>>>>>
>>>>>>>>>> Thanks for your reply. I solved this problem.
>>>>>>>>>>
>>>>>>>>>> I generated the build file as following:
>>>>>>>>>>
>>>>>>>>>> CHG CONTCAR EIGENVAL INCAR OSZICAR paral.qs.o889660 POSCAR  
>>>>>>>>>> REPORT wannier90.eig wannier90.win   WAVECAR
>>>>>>>>>> CHGCAR DOSCAR IBZKPT KPOINTS OUTCAR   PCDAT POTCAR 
>>>>>>>>>> vasprun.xml wannier90.mmn wannier90.wout  XDATCAR
>>>>>>>>>>
>>>>>>>>>> There is no error.
>>>>>>>>>>
>>>>>>>>>> which script do I need to read the .mmn file to plot the 
>>>>>>>>>> result? So far, the result file is empty.
>>>>>>>>>>
>>>>>>>>>> Regards
>>>>>>>>>> Vera
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> On Feb 8, 2017, at 11:16 AM, Dominik Gresch 
>>>>>>>>>>> <greschd at phys.ethz.ch <mailto:greschd at phys.ethz.ch>> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Dear Wei Li,
>>>>>>>>>>>
>>>>>>>>>>> It seems you are running multiple instances of the Python 
>>>>>>>>>>> interpreter, due to the 'mpirun' command. There seems to be 
>>>>>>>>>>> a bit of a race condition when they all try to create the 
>>>>>>>>>>> 'results' folder.
>>>>>>>>>>>
>>>>>>>>>>> In general, you shouldn't run Python itself with mpirun, 
>>>>>>>>>>> only the first-principles command (command="mpirun 
>>>>>>>>>>> YOUR_VASP_COMMAND" in the z2pack.fp.System options).
>>>>>>>>>>>
>>>>>>>>>>> Best regards,
>>>>>>>>>>>
>>>>>>>>>>> Dominik Gresch
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 08.02.2017 17:08, Wei Li wrote:
>>>>>>>>>>>> Dear Dominik Gresch,
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks a lot.
>>>>>>>>>>>>
>>>>>>>>>>>> I activated py35 and it works.
>>>>>>>>>>>>
>>>>>>>>>>>> Do I need to change any parameters if I want to run the 
>>>>>>>>>>>> example given here:
>>>>>>>>>>>> https://github.com/Z2PackDev/Z2Pack/tree/master/2.0.x/examples/fp/Bi_vasp
>>>>>>>>>>>>
>>>>>>>>>>>> I run it directly and I got the attached output, I did not 
>>>>>>>>>>>> find any error in output file or log file, but the process 
>>>>>>>>>>>> is terminated.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Regards
>>>>>>>>>>>> Wei Li
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> On Feb 8, 2017, at 4:53 AM, Dominik Gresch 
>>>>>>>>>>>>> <greschd at phys.ethz.ch <mailto:greschd at phys.ethz.ch>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Dear Wei Li,
>>>>>>>>>>>>>
>>>>>>>>>>>>> The python version on which you installed Z2Pack (3.5.2) 
>>>>>>>>>>>>> is probably not the same as you are using to run the 
>>>>>>>>>>>>> script. Since it seems you are using a virtualenv (py35) 
>>>>>>>>>>>>> when running Python from the command line, you should make 
>>>>>>>>>>>>> sure the same virtualenv is also active in your job (i.e., 
>>>>>>>>>>>>> "source py35/bin/activate" in your script).
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best regards,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Dominik Gresch
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 08.02.2017 10:31, Wei Li wrote:
>>>>>>>>>>>>>> Dear Z2pack team,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I have complied Wannier90 1.2 on top of VASP, and then I 
>>>>>>>>>>>>>> downloaded and installed z2pack like below:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> (py35) [verali at 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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