K-grid is not fully q-connected @ Q**

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Re: K-grid is not fully q-connected @ Q**

Postby martinspenke » Wed May 31, 2017 10:32 am

Dear Andrea and Davide,

I also have the exact problem with this warning since couple of months.
Attached you find an example (LiF) with a quick run; please change the number of q-points in ph.in and elph.in accordingly.

Here the output when I use ypp_ph :

Code: Select all
<01s> P0001: [01] CPU structure, Files & I/O Directories
 <01s> P0001: CPU-Threads:32(CPU)-1(threads)-1(threads@X)-1(threads@DIP)-1(threads@SE)-1(threads@RT)-1(threads@K)
 <01s> P0001: [02] Y(ambo) P(ost)/(re) P(rocessor)
 <01s> P0001: [03] Core DB
 <01s> P0001: :: Electrons             : 8.000000
 <01s> P0001: :: Temperature       [ev]: 0.000000
 <01s> P0001: :: Lattice factors [a.u.]: 7.188329  7.188329  7.188329
 <01s> P0001: :: K points              :  59
 <01s> P0001: :: Bands                 : 100
 <01s> P0001: :: Symmetries            : 16
 <01s> P0001: :: RL vectors            :  35557
 <01s> P0001: [04] K-point grid
 <01s> P0001: :: Q-points   (IBZ):  59
 <01s> P0001: :: X K-points (IBZ):  59
 <01s> P0001: [05] CORE Variables Setup
 <01s> P0001: [05.01] Unit cells
 <01s> P0001: [05.02] Symmetries
 <01s> P0001: [05.03] RL shells
 <01s> P0001: [05.04] K-grid lattice
 <01s> P0001: [05.05] Energies [ev] & Occupations
 <02s> P0001: [06] == Electron-Phonon Interface: PW->Yambo Databases ==
 <02s> P0001: PW(ELPH) databases ...
 <02s> P0001: [M  0.233 Gb] Alloc GKKP ( 0.229)
 <02s> P0001: [M  0.348 Gb] Alloc GKKP_DW ( 0.114)
 <02s> P0001: ELPH databases (WRITE) |                                        | [000%] --(E) --(X)
 <04s> P0001: [WARNING]K-grid is not fully q-connected @ Q1
 <16s> P0001: [WARNING]K-grid is not fully q-connected @ Q2
 <27s> P0001: ELPH databases (WRITE) |#                                       | [003%] 25s(E) 12m-34s(X)
 <28s> P0001: [WARNING]K-grid is not fully q-connected @ Q3
 <39s> P0001: ELPH databases (WRITE) |##                                      | [005%] 37s(E) 12m-15s(X)
 <40s> P0001: [WARNING]K-grid is not fully q-connected @ Q4
 <51s> P0001: [WARNING]K-grid is not fully q-connected @ Q5
 <59s> P0001: ELPH databases (WRITE) |###                                     | [008%] 57s(E) 11m-20s(X)
 <01m-00s> P0001: [WARNING]K-grid is not fully q-connected @ Q6
 <01m-08s> P0001: ELPH databases (WRITE) |####                                    | [010%] 01m-06s(E) 10m-55s(X)
 <01m-09s> P0001: [WARNING]K-grid is not fully q-connected @ Q7
 <01m-18s> P0001: [WARNING]K-grid is not fully q-connected @ Q8
 <01m-27s> P0001: ELPH databases (WRITE) |#####                                   | [013%] 01m-25s(E) 10m-28s(X)
 <01m-28s> P0001: [WARNING]K-grid is not fully q-connected @ Q9
 <01m-36s> P0001: ELPH databases (WRITE) |######                                  | [015%] 01m-34s(E) 10m-20s(X)
 <01m-37s> P0001: [WARNING]K-grid is not fully q-connected @ Q10
 <01m-47s> P0001: [WARNING]K-grid is not fully q-connected @ Q11
 <01m-55s> P0001: ELPH databases (WRITE) |#######                                 | [018%] 01m-53s(E) 10m-08s(X)
 <01m-56s> P0001: [WARNING]K-grid is not fully q-connected @ Q12
 <02m-05s> P0001: ELPH databases (WRITE) |########                                | [020%] 02m-02s(E) 10m-04s(X)
 <02m-05s> P0001: [WARNING]K-grid is not fully q-connected @ Q13
 <02m-15s> P0001: [WARNING]K-grid is not fully q-connected @ Q14
 <02m-23s> P0001: ELPH databases (WRITE) |#########                               | [023%] 02m-21s(E) 09m-56s(X)
 <02m-24s> P0001: [WARNING]K-grid is not fully q-connected @ Q15
 <02m-32s> P0001: ELPH databases (WRITE) |##########                              | [025%] 02m-30s(E) 09m-53s(X)
 <02m-33s> P0001: [WARNING]K-grid is not fully q-connected @ Q16
 <02m-42s> P0001: [WARNING]K-grid is not fully q-connected @ Q17
 <02m-51s> P0001: ELPH databases (WRITE) |###########                             | [028%] 02m-49s(E) 09m-47s(X)
 <02m-51s> P0001: [WARNING]K-grid is not fully q-connected @ Q18
 <03m-00s> P0001: ELPH databases (WRITE) |############                            | [030%] 02m-58s(E) 09m-45s(X)
 <03m-01s> P0001: [WARNING]K-grid is not fully q-connected @ Q19
 <03m-10s> P0001: [WARNING]K-grid is not fully q-connected @ Q20
 <03m-19s> P0001: ELPH databases (WRITE) |#############                           | [033%] 03m-17s(E) 09m-41s(X)
 <03m-19s> P0001: [WARNING]K-grid is not fully q-connected @ Q21
 <03m-28s> P0001: ELPH databases (WRITE) |##############                          | [035%] 03m-26s(E) 09m-39s(X)
 <03m-29s> P0001: [WARNING]K-grid is not fully q-connected @ Q22
 <03m-38s> P0001: [WARNING]K-grid is not fully q-connected @ Q23
 <03m-47s> P0001: ELPH databases (WRITE) |###############                         | [038%] 03m-44s(E) 09m-37s(X)
 <03m-47s> P0001: [WARNING]K-grid is not fully q-connected @ Q24
 <03m-56s> P0001: ELPH databases (WRITE) |################                        | [040%] 03m-54s(E) 09m-35s(X)
 <03m-57s> P0001: [WARNING]K-grid is not fully q-connected @ Q25
 <04m-06s> P0001: [WARNING]K-grid is not fully q-connected @ Q26
 <04m-14s> P0001: ELPH databases (WRITE) |#################                       | [044%] 04m-12s(E) 09m-33s(X)
 <04m-15s> P0001: [WARNING]K-grid is not fully q-connected @ Q27
 <04m-24s> P0001: ELPH databases (WRITE) |##################                      | [045%] 04m-22s(E) 09m-32s(X)
 <04m-24s> P0001: [WARNING]K-grid is not fully q-connected @ Q28
 <04m-34s> P0001: [WARNING]K-grid is not fully q-connected @ Q29
 <04m-42s> P0001: ELPH databases (WRITE) |###################                     | [049%] 04m-40s(E) 09m-30s(X)
 <04m-43s> P0001: [WARNING]K-grid is not fully q-connected @ Q30
 <04m-51s> P0001: ELPH databases (WRITE) |####################                    | [050%] 04m-49s(E) 09m-29s(X)
 <04m-52s> P0001: [WARNING]K-grid is not fully q-connected @ Q31
 <05m-00s> P0001: ELPH databases (WRITE) |#####################                   | [052%] 04m-58s(E) 09m-28s(X)
 <05m-01s> P0001: [WARNING]K-grid is not fully q-connected @ Q32
 <05m-10s> P0001: [WARNING]K-grid is not fully q-connected @ Q33
 <05m-19s> P0001: ELPH databases (WRITE) |######################                  | [055%] 05m-17s(E) 09m-27s(X)
 <05m-20s> P0001: [WARNING]K-grid is not fully q-connected @ Q34
 <05m-28s> P0001: ELPH databases (WRITE) |#######################                 | [057%] 05m-26s(E) 09m-26s(X)
 <05m-29s> P0001: [WARNING]K-grid is not fully q-connected @ Q35
 <05m-38s> P0001: [WARNING]K-grid is not fully q-connected @ Q36
 <05m-47s> P0001: ELPH databases (WRITE) |########################                | [061%] 05m-45s(E) 09m-26s(X)
 <05m-48s> P0001: [WARNING]K-grid is not fully q-connected @ Q37
 <05m-57s> P0001: ELPH databases (WRITE) |#########################               | [062%] 05m-55s(E) 09m-26s(X)
 <05m-57s> P0001: [WARNING]K-grid is not fully q-connected @ Q38
 <06m-07s> P0001: [WARNING]K-grid is not fully q-connected @ Q39
 <06m-16s> P0001: ELPH databases (WRITE) |##########################              | [066%] 06m-14s(E) 09m-26s(X)
 <06m-17s> P0001: [WARNING]K-grid is not fully q-connected @ Q40
 <06m-26s> P0001: ELPH databases (WRITE) |###########################             | [067%] 06m-24s(E) 09m-26s(X)
 <06m-27s> P0001: [WARNING]K-grid is not fully q-connected @ Q41
 <06m-36s> P0001: [WARNING]K-grid is not fully q-connected @ Q42
 <06m-45s> P0001: ELPH databases (WRITE) |############################            | [071%] 06m-43s(E) 09m-26s(X)
 <06m-46s> P0001: [WARNING]K-grid is not fully q-connected @ Q43
 <06m-55s> P0001: ELPH databases (WRITE) |#############################           | [072%] 06m-52s(E) 09m-26s(X)
 <06m-55s> P0001: [WARNING]K-grid is not fully q-connected @ Q44
 <07m-04s> P0001: [WARNING]K-grid is not fully q-connected @ Q45
 <07m-13s> P0001: ELPH databases (WRITE) |##############################          | [076%] 07m-11s(E) 09m-25s(X)
 <07m-14s> P0001: [WARNING]K-grid is not fully q-connected @ Q46
 <07m-22s> P0001: ELPH databases (WRITE) |###############################         | [077%] 07m-20s(E) 09m-24s(X)
 <07m-23s> P0001: [WARNING]K-grid is not fully q-connected @ Q47
 <07m-32s> P0001: [WARNING]K-grid is not fully q-connected @ Q48
 <07m-41s> P0001: ELPH databases (WRITE) |################################        | [081%] 07m-39s(E) 09m-24s(X)
 <07m-41s> P0001: [WARNING]K-grid is not fully q-connected @ Q49
 <07m-50s> P0001: ELPH databases (WRITE) |#################################       | [083%] 07m-48s(E) 09m-23s(X)
 <07m-51s> P0001: [WARNING]K-grid is not fully q-connected @ Q50
 <08m-00s> P0001: [WARNING]K-grid is not fully q-connected @ Q51
 <08m-09s> P0001: ELPH databases (WRITE) |##################################      | [086%] 08m-06s(E) 09m-23s(X)
 <08m-09s> P0001: [WARNING]K-grid is not fully q-connected @ Q52
 <08m-18s> P0001: ELPH databases (WRITE) |###################################     | [088%] 08m-16s(E) 09m-23s(X)
 <08m-19s> P0001: [WARNING]K-grid is not fully q-connected @ Q53
 <08m-28s> P0001: [WARNING]K-grid is not fully q-connected @ Q54
 <08m-36s> P0001: ELPH databases (WRITE) |####################################    | [091%] 08m-34s(E) 09m-22s(X)
 <08m-37s> P0001: [WARNING]K-grid is not fully q-connected @ Q55
 <08m-46s> P0001: ELPH databases (WRITE) |#####################################   | [093%] 08m-44s(E) 09m-22s(X)
 <08m-46s> P0001: [WARNING]K-grid is not fully q-connected @ Q56
 <08m-56s> P0001: [WARNING]K-grid is not fully q-connected @ Q57
 <09m-04s> P0001: ELPH databases (WRITE) |######################################  | [096%] 09m-02s(E) 09m-21s(X)
 <09m-05s> P0001: [WARNING]K-grid is not fully q-connected @ Q58
 <09m-14s> P0001: ELPH databases (WRITE) |####################################### | [098%] 09m-12s(E) 09m-21s(X)
 <09m-14s> P0001: [WARNING]K-grid is not fully q-connected @ Q59
 <09m-23s> P0001: ELPH databases (WRITE) |########################################| [100%] 09m-21s(E) 09m-21s(X)
 <09m-23s> P0001: :: Modes           :  6
 <09m-23s> P0001: :: Bands range     : 100
 <09m-23s> P0001: [07] Game Over





Best wishes,
Martin
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Martin Spenke, PhD Student
Theoretisch-Physikalisches Institut
Universität Hamburg, Germany
martinspenke
 
Posts: 149
Joined: Tue Apr 08, 2014 6:05 am

Re: K-grid is not fully q-connected @ Q**

Postby elena.cannuccia » Thu Jun 01, 2017 4:23 pm

Ciao Andrea,

thanks for your reply.
Well, as you suggested I tried to reproduce the warning reducing the cutoff (ecut=10Ry and thr2_ph=10^-10).
The grid is 4x4x2. This is the best I could do. I hope you are able to run it in a relatively short lapse of time.

Here the calculation in a dropbox folder
https://www.dropbox.com/s/nrvwkc6bl6z49 ... ar.gz?dl=0

In the main directory there is a *dvscf and *elph files with their respective log files.
The elph_dir is the folder where the databases (s.db*) have been created by ph.x, and where I run yambo_ph and ypp_ph to create the database for an el-ph calculation.

Elena
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Re: K-grid is not fully q-connected @ Q**

Postby Davide Sangalli » Thu Jun 01, 2017 11:17 pm

Ciao Elena,
I did a test with the databases from your dropbox folder.
Indeed I get the same warning message. It originates from the following:
the system has in total 8 (32) kpts in the IBZ (BZ)

ypp_ph creates a table "k_found" of size 32 (=nk BZ) and then reads the number of kpts in the s.dbph_ file
The values of such files are:
Code: Select all
iq  elph_nk   nk_from_elph_log
1     2              8
2     2             16
3     5             40
4     5             40
5     4             28
6     4             28
7     8             64
8     8             64


There is a mismatch in between the number printed inside the s.dbph_* file and the output from the elph run with ph.x
My best guess is that the printing of the s.dbph_* databases is not working properly when ph.x is run parallelizing over pools.
Can you try without pools ?

D.

P.S.: For Martin. I have the impression you are still using the old procedure, giving the list of q-points in input to ph.x
While this is in principle possible, it can easily give some errors. The new suggested procedure is to run ph.x with l_disp=.true. and setting a q-grid there.
You can check the input files provided by Elena.
Then you just need to let yambo read the q points from the produced s.dbph_* databases, putting the SAVE folder inside the elph_dir generated by ph.x before doing the setup/initialization.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
http://www.ism.cnr.it/en/davide-sangalli-cv/
http://www.max-centre.eu/
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Re: K-grid is not fully q-connected @ Q**

Postby elena.cannuccia » Fri Jun 02, 2017 9:25 am

Thank you Davide!

It really seems to work now.

Elena
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Posts: 17
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Re: K-grid is not fully q-connected @ Q**

Postby martinspenke » Fri Jun 02, 2017 9:39 am

Dear Davide,

Yes, but I like to work with randomly generated q-points to speed up the convergence as suggested in the tutorial.

Best,
Martin
Martin Spenke, PhD Student
Theoretisch-Physikalisches Institut
Universität Hamburg, Germany
martinspenke
 
Posts: 149
Joined: Tue Apr 08, 2014 6:05 am

Re: K-grid is not fully q-connected @ Q**

Postby Davide Sangalli » Fri Jun 02, 2017 9:45 am

I see.
Then I think it is natural you get the warning message.
I'm not a big expert of yambo_ph calculations however.
Does it give any problem with the calculations in practice ?

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
http://www.ism.cnr.it/en/davide-sangalli-cv/
http://www.max-centre.eu/
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Re: K-grid is not fully q-connected @ Q**

Postby martinspenke » Fri Jun 02, 2017 6:23 pm

Dear Davide,

I think results are reasonable even with this warning.

Bests,
Martin
Martin Spenke, PhD Student
Theoretisch-Physikalisches Institut
Universität Hamburg, Germany
martinspenke
 
Posts: 149
Joined: Tue Apr 08, 2014 6:05 am

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