BSE: Screened interaction matrix calculation

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Moderators: Daniele Varsano, andrea.ferretti, andrea marini, Conor Hogan, myrta gruning

BSE: Screened interaction matrix calculation

Postby Evgeniia » Wed Apr 11, 2018 1:12 pm

Hi all. I am trying to repeat the BSE calculation for the cubic perovskite cell. Currently I got stuck on the calculation of statically screened electron-electron interaction. The problem is the following: I run the W1.in with the parmeter NGsBlkXS=51. In the output file 1) the size of my matrix is changed 2) in the end, where there is the input file text, I see that the parameter is changed also! I tried to take the text of the input from the end of r_em1s_1 file, changed the parameter and ran the input again. The result was the same - in the new output the size of the matrix was different, and the text of the input differs from what I really had. I think that due to this my BSE calculation does not work - it gives NetCDF problems of different types all the time.

Before writing here, I tried to repeat the LiF tutorial and then I tried NaCl. In both cases I succeeded in BSE calculation, and no problems appeared with the X-matrix.
Could you please help me with that?
My first input is:

em1s # [R Xs] Static Inverse Dielectric Matrix
X_Threads= 4 # [OPENMP/X] Number of threads for response functions
DIP_Threads= 4 # [OPENMP/X] Number of threads for dipoles
Chimod= "Hartree" # [X] IP/Hartree/ALDA/LRC/BSfxc
%QpntsRXs
1|20| # (Xs) Transferred momenta
%
% BndsRnXs
9 | 35 | # [Xs] Polarization function bands
%
NGsBlkXs= 51 RL # [Xs] Response block size
% DmRngeXs
0.10000 | 0.10000 | eV # [Xs] Damping range
%
% LongDrXs
1.000000 | 0.000000 | 0.000000 | cc # [Xs] Electric Field
%

The output is:


GPL Version 4.0.4 Revision 107
Serial+OpenMP Build
http://www.yambo-code.org

04/11/2018 at 15:08 YAMBO @ iivrubel-mint

[01] CPU structure, Files & I/O Directories
===========================================

* CPU-Threads :1(CPU)-4(threads)-4(threads@X)-4(threads@DIP)
* MPI CPU : 1
* THREADS (max): 4
* THREADS TOT(max): 4
* I/O NODES : 1
* Fragmented WFs :yes

CORE databases in .
Additional I/O in .
Communications in .
Input file is W1.in
Report file is ./r_em1s

[RD./SAVE//ns.db1]------------------------------------------
Bands : 35
K-points : 20
G-vectors [RL space]: 138217
Components [wavefunctions]: 17352
Symmetries [spatial]: 48
Spinor components : 1
Spin polarizations : 1
Temperature [ev]: 0.000000
Electrons : 36.00000
WF G-vectors : 20173
Max atoms/species : 3
No. of atom species : 3
Magnetic symmetries : no
- S/N 009539 --------------------------- v.04.00.04 r.0107 -

[02] CORE Variables Setup
=========================


[02.01] Unit cells
==================

Unit cell is CUB

... containing 1Cs1Pb3Br atoms

... with scaling factors [a.u.]: 11.26277 11.26277 11.26277

Direct Lattice(DL) unit cell [iru / cc(a.u.)]
A1 = 1.000000 0.000000 0.000000 11.26277 0.000000 0.000000
A2 = 0.000000 1.000000 0.000000 0.000000 11.26277 0.000000
A3 = 0.000000 0.000000 1.000000 0.000000 0.000000 11.26277

DL volume [au]: 1429.

Reciprocal Lattice(RL) unit cell [iku / cc]
B1 = 1.000000 0.000000 0.000000 0.557872 0.000000 0.000000
B2 = 0.000000 1.000000 0.000000 0.000000 0.557872 0.000000
B3 = 0.000000 0.000000 1.000000 0.000000 0.000000 0.557872


[02.02] Symmetries
==================

DL (S)ymmetries [cc]
[S1] 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000
[S2]-1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 1.000000
[S3]-1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000
[S4] 1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000
[S5] 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 -1.000000
[S6] 0.000000 -1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 -1.000000
[S7] 0.000000 -1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000
[S8] 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 1.000000
[S9] 0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 1.000000 0.000000 0.000000
[S10] 0.000000 0.000000 -1.000000 0.000000 -1.000000 0.000000 -1.000000 0.000000 0.000000
[S11] 0.000000 0.000000 -1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000
[S12] 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000
[S13]-1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000
[S14]-1.000000 0.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 -1.000000 0.000000
[S15] 1.000000 0.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 1.000000 0.000000
[S16] 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000
[S17] 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000
[S18] 0.000000 0.000000 -1.000000 -1.000000 0.000000 0.000000 0.000000 1.000000 0.000000
[S19] 0.000000 0.000000 -1.000000 1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000
[S20] 0.000000 0.000000 1.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000
[S21] 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000
[S22] 0.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000 1.000000 0.000000 0.000000
[S23] 0.000000 -1.000000 0.000000 0.000000 0.000000 1.000000 -1.000000 0.000000 0.000000
[S24] 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000 -1.000000 0.000000 0.000000
[S25]-1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000
[S26] 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000
[S27] 1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 1.000000
[S28]-1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000
[S29] 0.000000 -1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 1.000000
[S30] 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000
[S31] 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 -1.000000
[S32] 0.000000 -1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 -1.000000
[S33] 0.000000 0.000000 -1.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000
[S34] 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000
[S35] 0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 -1.000000 0.000000 0.000000
[S36] 0.000000 0.000000 -1.000000 0.000000 -1.000000 0.000000 1.000000 0.000000 0.000000
[S37] 1.000000 0.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 -1.000000 0.000000
[S38] 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000
[S39]-1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000
[S40]-1.000000 0.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 1.000000 0.000000
[S41] 0.000000 0.000000 -1.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000
[S42] 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000
[S43] 0.000000 0.000000 1.000000 -1.000000 0.000000 0.000000 0.000000 1.000000 0.000000
[S44] 0.000000 0.000000 -1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000
[S45] 0.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000 -1.000000 0.000000 0.000000
[S46] 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -1.000000 0.000000 0.000000
[S47] 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000 1.000000 0.000000 0.000000
[S48] 0.000000 -1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000

[SYMs] K-space Time-reversal not included
[SYMs] Spatial inversion 25 is a symmetry
[SYMs] Group table built correctly

[02.03] RL shells
=================

Shells, format: [S#] G_RL(mHa)

[S33]:949( 5758.) [S32]:925( 5602.) [S31]:895( 5446.) [S30]:847( 5291.)
[S29]:799( 5135.) [S28]:751( 4980.) [S27]:739( 4668.) [S26]:691( 4513.)
[S25]:619( 4201.) [S24]:587( 4046.) [S23]:515( 3890.) [S22]:485( 3735.)
[S21]:461( 3423.) [S20]:437( 3268.) [S19]:389( 3112.) [S18]:365( 2957.)
[S17]:341( 2801.) [S16]:305( 2645.) [S15]:257( 2490.) [S14]:251( 2179.)
[S13]:203( 2023.) [S12]:179( 1867.) [S11]:171( 1712.) [S10]:147( 1556.)
[S9]:123( 1400.) [S8]:93( 1245.) [S7]:81( 933.6642) [S6]:57( 778.0535)
...
[S12]:179( 1867.) [S11]:171( 1712.) [S10]:147( 1556.) [S9]:123( 1400.)
[S8]:93( 1245.) [S7]:81( 933.6642) [S6]:57( 778.0535) [S5]:33( 622.4429)
[S4]:27( 466.8322) [S3]:19( 311.2214) [S2]:7( 155.6107) [S1]:1( 0.000000)

[02.04] K-grid lattice
======================

Compatible Grid is 3D
B1 [rlu]= 0.000000 -0.166667 0.000000
B2 =-0.166667 0.000000 0.000000
B3 = 0.000000 0.000000 -0.166667
Grid dimensions : 6 6 6
K lattice UC volume [au]:0.8038E-3

[02.05] Energies [ev] & Occupations
===================================

Fermi Level [ev]: 1.819997
VBM / CBm [ev]: 0.000000 1.758880
Electronic Temp. [ev K]: 0.00 0.00
Bosonic Temp. [ev K]: 0.00 0.00
El. density [cm-3]: 0.170E+24
States summary : Full Metallic Empty
0001-0018 0019-0035
Indirect Gaps [ev]: 1.758880 3.516209
Direct Gaps [ev]: 1.758880 5.562145
X BZ K-points : 216

Energy unit is electronVolt [eV]

*X* K [1] : 0.000000 0.000000 0.000000 ( cc) * Comp.s 17269 * weight 0.0046
0.000000 0.000000 0.000000 (rlu)
E -16.65452 -16.65452 -16.53349 -16.53349 -16.53349 -14.40508 -13.78592 -13.78592
E -6.827471 -3.917402 -3.917402 -3.917402 -1.816826 -1.816826 -1.816826 -1.754031
E -1.754031 -1.754031 3.274589 4.450490 4.450490 5.205429 5.205429 5.205429
E 5.930813 5.930813 5.930813 8.039851 8.039851 8.039852 9.697020 9.697021
E 9.69703 10.50889 10.50891

*X* K [2] : 0.000000 0.000000 0.09298 ( cc) * Comp.s 17276 * weight 0.02778
0.000000 0.000000 0.166667 (rlu)
E -16.65451 -16.64241 -16.53367 -16.53367 -16.53348 -14.37659 -13.83470 -13.78562
E -7.037754 -3.891314 -3.891314 -3.465448 -1.848952 -1.848952 -1.845183 -1.775019
E -1.775019 -1.757329 3.512089 4.588560 4.650308 5.125516 5.292518 5.302124
E 5.302124 5.946032 5.946033 7.649233 8.129833 8.129835 8.878403 9.543946
E 9.54395 9.91098 10.47087

*X* K [3] : 0.000000 0.000000 0.185957 ( cc) * Comp.s 17204 * weight 0.02778
0.000000 0.000000 0.333333 (rlu)
E -16.65448 -16.61781 -16.53405 -16.53405 -16.53348 -14.29463 -13.95782 -13.78500
E -7.356430 -3.835979 -3.835979 -2.678041 -1.933748 -1.933748 -1.900055 -1.798635
E -1.798635 -1.591235 3.515414 4.197958 4.947417 5.123798 5.369865 5.369865
E 5.529585 6.274890 6.274891 6.990861 7.604262 7.861674 7.861681 8.867046
E 9.633987 9.633998 9.689672

*X* K [4] : 0.000000 0.000000 -0.278936 ( cc) * Comp.s 17240 * weight 0.01389
0.000000 0.000000 -0.500000 (rlu)
E -16.65446 -16.60532 -16.53424 -16.53424 -16.53347 -14.21269 -14.06073 -13.78469
E -7.485482 -3.806485 -3.806485 -2.429378 -1.980556 -1.980556 -1.926634 -1.807395
E -1.807395 -1.239884 2.706644 4.679873 5.097960 5.355380 5.355382 5.423332
E 5.727171 6.629555 6.796352 6.796354 6.935760 7.293010 7.293010 8.359301
E 9.138572 9.947140 9.947148

*X* K [5] : 0.000000 0.09298 0.09298 ( cc) * Comp.s 17245 * weight 0.05556
0.000000 0.166667 0.166667 (rlu)
E -16.64851 -16.63613 -16.53386 -16.53367 -16.53367 -14.34980 -13.85480 -13.81131
E -7.231067 -3.864187 -3.577433 -3.318394 -2.001037 -1.868598 -1.814418 -1.809388
E -1.765546 -1.698816 3.713034 4.720710 4.729199 4.993860 5.008991 5.269549
E 5.471962 5.812389 5.943830 7.565441 7.907270 8.228309 8.826030 9.037866
E 9.22868 9.74259 10.28013

*X* K [6] : 0.000000 0.09298 0.185957 ( cc) * Comp.s 17236 * weight 0.111111
0.000000 0.166667 0.333333 (rlu)
E -16.64637 -16.61335 -16.53424 -16.53405 -16.53366 -14.27244 -13.96160 -13.82064
E -7.532991 -3.806475 -3.433667 -2.661149 -2.115834 -1.942408 -1.846208 -1.828190
E -1.703919 -1.541555 3.410151 4.305329 4.742991 5.106771 5.246333 5.272827
E 5.718007 6.192869 6.277576 7.122403 7.238642 8.020244 8.088813 8.826157
E 9.21944 9.34477 10.12710

*X* K [7] : 0.000000 0.09298 -0.278936 ( cc) * Comp.s 17254 * weight 0.05556
0.000000 0.166667 -0.500000 (rlu)
E -16.64611 -16.60094 -16.53443 -16.53424 -16.53366 -14.19301 -14.06007 -13.82136
E -7.657424 -3.775607 -3.392452 -2.487098 -2.114931 -1.988888 -1.856646 -1.829674
E -1.697632 -1.182581 2.594537 4.573158 4.866965 5.219194 5.256646 5.540576
E 5.856041 6.437666 6.577870 6.633471 7.280969 7.415890 7.596189 8.408365
E 9.439393 9.452801 9.855403

*X* K [8] : 0.000000 0.185957 0.185957 ( cc) * Comp.s 17261 * weight 0.05556
0.000000 0.333333 0.333333 (rlu)
E -16.63673 -16.59741 -16.53463 -16.53404 -16.53404 -14.20721 -13.99076 -13.89191
E -7.818185 -3.743257 -2.746297 -2.615436 -2.214605 -1.966828 -1.937837 -1.866202
E -1.513081 -1.319771 3.181698 3.251637 4.842669 5.087348 5.450688 5.641822
E 6.062524 6.212963 6.223335 6.724649 7.292795 7.870006 8.549540 8.623175
E 8.76025 8.78952 10.40977

*X* K [9] : 0.000000 0.185957 -0.278936 ( cc) * Comp.s 17278 * weight 0.05556
0.000000 0.333333 -0.500000 (rlu)
E -16.63443 -16.58669 -16.53482 -16.53423 -16.53404 -14.13385 -14.05874 -13.91529
E -7.938272 -3.709150 -2.601490 -2.569772 -2.149059 -2.005387 -1.959492 -1.885476
E -1.469792 -0.936699 2.371941 3.129605 5.022867 5.367566 5.400475 5.826516
E 6.174400 6.385791 6.396804 6.405490 7.212231 7.534351 8.222147 8.462245
E 8.56032 9.59993 10.07481

*X* K [10] : 0.000000 -0.278936 -0.278936 ( cc) * Comp.s 17292 * weight 0.01389
0.000000 -0.500000 -0.500000 (rlu)
E -16.63096 -16.57696 -16.53501 -16.53423 -16.53423 -14.05807 -14.05807 -14.00886
E -8.057418 -3.673103 -2.653289 -2.148328 -2.148328 -2.013557 -2.013557 -1.955752
E -1.375919 -0.604464 2.261214 2.261214 4.947287 5.447054 5.755743 5.988487
E 6.398753 6.398753 6.404135 6.404135 7.120991 7.125548 8.139121 8.139121
E 9.43540 9.43542 10.08793

*X* K [11] : 0.09298 0.09298 0.09298 ( cc) * Comp.s 17236 * weight 0.03704
0.166667 0.166667 0.166667 (rlu)
E -16.63612 -16.63612 -16.53386 -16.53386 -16.53386 -14.32488 -13.85452 -13.85452
E -7.411905 -3.548413 -3.548413 -3.188279 -2.027455 -2.027455 -1.864192 -1.713050
E -1.701436 -1.701436 3.860709 4.658525 4.658526 4.890889 5.033428 5.033429
E 5.770329 5.770330 5.947646 7.395729 8.161958 8.161958 8.309506 8.908351
E 8.908353 9.939906 9.939910

*X* K [12] : 0.09298 0.09298 0.185957 ( cc) * Comp.s 17279 * weight 0.111111
0.166667 0.166667 0.333333 (rlu)
E -16.63610 -16.61093 -16.53424 -16.53424 -16.53386 -14.25247 -13.96428 -13.85399
E -7.700978 -3.485128 -3.331457 -2.647056 -2.197156 -2.052490 -1.825411 -1.715004
E -1.655699 -1.524806 3.300533 4.278618 4.509792 4.793126 5.255306 5.367549
E 5.935424 6.249514 6.331158 6.826586 7.558393 7.765813 8.202368 8.781590
E 8.95800 9.42797 10.09042

*X* K [13] : 0.09298 0.09298 -0.278936 ( cc) * Comp.s 17266 * weight 0.05556
0.166667 0.166667 -0.500000 (rlu)
E -16.63609 -16.59812 -16.53443 -16.53443 -16.53385 -14.17627 -14.05952 -13.85372
E -7.821851 -3.450171 -3.278949 -2.508694 -2.269196 -2.007742 -1.826876 -1.720056
E -1.645064 -1.139606 2.480434 4.404975 4.447587 4.947118 5.442716 5.662703
E 6.050005 6.363578 6.379066 6.640144 7.506197 7.542581 7.576857 8.647705
E 9.154790 9.501950 9.904043

*X* K [14] : 0.09298 0.185957 0.185957 ( cc) * Comp.s 17264 * weight 0.111111
0.166667 0.333333 0.333333 (rlu)
E -16.62379 -16.59740 -16.53462 -16.53423 -16.53423 -14.19343 -13.99051 -13.91962
E -7.977089 -3.355532 -2.720100 -2.606106 -2.306540 -2.160553 -1.770808 -1.680910
E -1.511999 -1.316403 3.063792 3.139005 4.259225 4.934327 5.564787 5.570217
E 6.195010 6.327367 6.368651 6.597429 7.593407 7.740091 8.375000 8.466043
E 8.728052 9.414128 9.994998

*X* K [15] : 0.09298 0.185957 -0.278936 ( cc) * Comp.s 17252 * weight 0.111111
0.166667 0.333333 -0.500000 (rlu)
E -16.62162 -16.58641 -16.53481 -16.53442 -16.53423 -14.12541 -14.05840 -13.93657
E -8.094711 -3.312960 -2.587993 -2.557669 -2.341779 -2.117183 -1.770513 -1.695986
E -1.465956 -0.904546 2.252666 3.012078 4.200696 5.192163 5.583546 5.945576
E 6.036184 6.047900 6.510063 6.910732 7.326941 7.711349 8.082249 8.523563
E 8.876491 9.572858 9.895546

*X* K [16] : 0.09298 -0.278936 -0.278936 ( cc) * Comp.s 17252 * weight 0.02778
0.166667 -0.500000 -0.500000 (rlu)
E -16.61773 -16.57695 -16.53501 -16.53442 -16.53442 -14.05784 -14.05784 -14.02056
E -8.211736 -3.267415 -2.633718 -2.348995 -2.348995 -1.954391 -1.763772 -1.763772
E -1.374370 -0.557074 2.138607 2.138607 4.111381 5.393115 5.662147 5.879309
E 5.879309 6.121084 7.012598 7.055770 7.055770 7.542491 8.208778 8.208779
E 9.400727 9.853969 9.854000

*X* K [17] : 0.185957 0.185957 0.185957 ( cc) * Comp.s 17307 * weight 0.03704
0.333333 0.333333 0.333333 (rlu)
E -16.59739 -16.59739 -16.53462 -16.53461 -16.53461 -14.15162 -13.99008 -13.99008
E -8.244233 -2.647408 -2.647408 -2.584781 -2.363829 -2.363829 -1.533465 -1.533465
E -1.490155 -1.136194 2.844555 2.844555 2.982059 4.934731 5.632334 5.632335
E 5.883205 6.426908 6.426910 7.054635 7.812538 7.812542 8.405266 8.405269
E 8.98762 9.37427 10.49131

*X* K [18] : 0.185957 0.185957 -0.278936 ( cc) * Comp.s 17260 * weight 0.05556
0.333333 0.333333 -0.500000 (rlu)
E -16.59738 -16.58393 -16.53481 -16.53480 -16.53461 -14.09865 -14.05773 -13.98982
E -8.359870 -2.572419 -2.561367 -2.527668 -2.493536 -2.178283 -1.533601 -1.521134
E -1.438914 -0.703411 2.011135 2.741944 2.848881 5.000513 5.552162 5.690088
E 5.741837 6.304933 6.715367 7.393754 7.498377 8.006503 8.349973 8.516402
E 9.12119 9.43108 10.39117

*X* K [19] : 0.185957 -0.278936 -0.278936 ( cc) * Comp.s 17304 * weight 0.02778
0.333333 -0.500000 -0.500000 (rlu)
E -16.59073 -16.57695 -16.53500 -16.53480 -16.53480 -14.05742 -14.05742 -14.04473
E -8.475345 -2.593890 -2.515453 -2.515453 -2.408536 -1.951665 -1.488665 -1.488665
E -1.371262 -0.345895 1.888048 1.888048 2.697741 4.933302 5.563376 5.568976
E 5.568977 6.469733 6.819021 7.635743 7.635744 7.965344 8.545268 8.545274
E 8.91380 9.96945 10.71694

*X* K [20] :-0.278936 -0.278936 -0.278936 ( cc) * Comp.s 17352 * weight 0.0046
-0.500000 -0.500000 -0.500000 (rlu)
E -16.57694 -16.57694 -16.53499 -16.53499 -16.53499 -14.05722 -14.05722 -14.05722
E -8.590828 -2.573620 -2.573620 -2.573620 -1.950300 -1.950300 -1.369704 -1.369704
E -1.369704 0.000000 1.758880 1.758880 1.758880 4.756520 5.465809 5.465809
E 5.465810 6.734022 6.734023 7.937470 7.937470 7.937472 8.748902 8.748908
E 8.74892 10.44043 10.91291

[03] Transferred momenta grid
=============================

[RD./SAVE//ndb.kindx]---------------------------------------
Fragmentation :no
Polarization last K : 20
QP states : 1 20
X grid is uniform :yes
X grid impose -q :no
BS scattering :no
COLL scattering :no
- S/N 009539 --------------------------- v.04.00.04 r.0107 -

IBZ Q-points : 20
BZ Q-points : 216

Q [00001] : 0.00 0.00 0.00 (iku) * weight 0.0046
Q [00002] : 0.000000 0.000000 0.166667 (iku) * weight 0.02778
Q [00003] : 0.000000 0.000000 0.333333 (iku) * weight 0.02778
Q [00004] : 0.000000 0.000000 -0.500000 (iku) * weight 0.01389
Q [00005] : 0.000000 0.166667 0.166667 (iku) * weight 0.05556
Q [00006] : 0.000000 0.166667 0.333333 (iku) * weight 0.111111
Q [00007] : 0.000000 0.166667 -0.500000 (iku) * weight 0.05556
Q [00008] : 0.000000 0.333333 0.333333 (iku) * weight 0.05556
Q [00009] : 0.000000 0.333333 -0.500000 (iku) * weight 0.05556
Q [00010] : 0.000000 -0.500000 -0.500000 (iku) * weight 0.01389
Q [00011] : 0.166667 0.166667 0.166667 (iku) * weight 0.03704
Q [00012] : 0.166667 0.166667 0.333333 (iku) * weight 0.111111
Q [00013] : 0.166667 0.166667 -0.500000 (iku) * weight 0.05556
Q [00014] : 0.166667 0.333333 0.333333 (iku) * weight 0.111111
Q [00015] : 0.166667 0.333333 -0.500000 (iku) * weight 0.111111
Q [00016] : 0.166667 -0.500000 -0.500000 (iku) * weight 0.02778
Q [00017] : 0.333333 0.333333 0.333333 (iku) * weight 0.03704
Q [00018] : 0.333333 0.333333 -0.500000 (iku) * weight 0.05556
Q [00019] : 0.333333 -0.500000 -0.500000 (iku) * weight 0.02778
Q [00020] :-0.500000 -0.500000 -0.500000 (iku) * weight 0.0046

Q [00001] : 0.00 0.00 0.00 (cc ) * weight 0.0046
Q [00002] : 0.000000 0.000000 0.092979 (cc ) * weight 0.02778
Q [00003] : 0.000000 0.000000 0.185957 (cc ) * weight 0.02778
Q [00004] : 0.000000 0.000000 -0.278936 (cc ) * weight 0.01389
Q [00005] : 0.000000 0.092979 0.092979 (cc ) * weight 0.05556
Q [00006] : 0.000000 0.092979 0.185957 (cc ) * weight 0.111111
Q [00007] : 0.000000 0.092979 -0.278936 (cc ) * weight 0.05556
Q [00008] : 0.000000 0.185957 0.185957 (cc ) * weight 0.05556
Q [00009] : 0.000000 0.185957 -0.278936 (cc ) * weight 0.05556
Q [00010] : 0.000000 -0.278936 -0.278936 (cc ) * weight 0.01389
Q [00011] : 0.092979 0.092979 0.092979 (cc ) * weight 0.03704
Q [00012] : 0.092979 0.092979 0.185957 (cc ) * weight 0.111111
Q [00013] : 0.092979 0.092979 -0.278936 (cc ) * weight 0.05556
Q [00014] : 0.092979 0.185957 0.185957 (cc ) * weight 0.111111
Q [00015] : 0.092979 0.185957 -0.278936 (cc ) * weight 0.111111
Q [00016] : 0.092979 -0.278936 -0.278936 (cc ) * weight 0.02778
Q [00017] : 0.185957 0.185957 0.185957 (cc ) * weight 0.03704
Q [00018] : 0.185957 0.185957 -0.278936 (cc ) * weight 0.05556
Q [00019] : 0.185957 -0.278936 -0.278936 (cc ) * weight 0.02778
Q [00020] :-0.278936 -0.278936 -0.278936 (cc ) * weight 0.0046

[04] External corrections
=========================


[05] Static Dielectric Matrix
=============================

[WR./SAVE//ndb.em1s]----------------------------------------
Brillouin Zone Q/K grids (IBZ/BZ): 20 216 20 216
RL vectors (WF): 949
Coulomb cutoff potential :none
Fragmentation :yes
Electronic Temperature [K]: 0.000000
Bosonic Temperature [K]: 0.000000
Static diel. fun. energies :Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
wavefunctions :Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
Global Gauge :length
X matrix size : 57
X band range : 9 35
X e/h energy range [ev]:-1.000000 -1.000000
X Time ordering :t
X xc-Kernel :none
X Drude frequency : 0.00 0.00
X poles [o/o]: 100.0000
Rl vectors in the sum :0
[r,Vnl] included :yes
Field direction :0.1000E-4 0.000 0.000
BZ energy Double Grid :no
BZ energy DbGd points :0
- S/N 009539 --------------------------- v.04.00.04 r.0107 -
[RD./SAVE//ndb.em1s]----------------------------------------
Brillouin Zone Q/K grids (IBZ/BZ): 20 216 20 216
RL vectors (WF): 949
Coulomb cutoff potential :none
Fragmentation :yes
Electronic Temperature [K]: 0.000000
Bosonic Temperature [K]: 0.000000
Static diel. fun. energies :Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
wavefunctions :Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
Global Gauge :length
X matrix size : 57
X band range : 9 35
X e/h energy range [ev]:-1.000000 -1.000000
X Time ordering :t
X xc-Kernel :none
X Drude frequency : 0.00 0.00
X poles [o/o]: 100.0000
Rl vectors in the sum :0
[r,Vnl] included :yes
Field direction :0.1000E-4 0.000 0.000
BZ energy Double Grid :no
BZ energy DbGd points :0
- S/N 009539 --------------------------- v.04.00.04 r.0107 -
[RD./SAVE//ns.kb_pp_pwscf]----------------------------------
Fragmentation :yes
- S/N 009539 --------------------------- v.04.00.04 r.0107 -

[WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
[WF] Performing Wave-Functions I/O from ./SAVE

[WF loader] Normalization (few states) min/max :0.1034E-8 0.9999

[WR./SAVE//ndb.dip_iR_and_P]--------------------------------
Brillouin Zone Q/K grids (IBZ/BZ): 20 216 20 216
RL vectors (WF): 949
Fragmentation :yes
Electronic Temperature [K]: 0.000000
Bosonic Temperature [K]: 0.000000
X band range : 9 35
X band range limits : 18 19
X e/h energy range [ev]:-1.000000 -1.000000
RL vectors in the sum : 949
[r,Vnl] included :yes
Using shifted grids :no
Using covariant dipoles:no
Using G-space approach :yes
Using R-space approach :no
Direct v evaluation :no
Field momentum norm :0.1000E-4
Wavefunctions :Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
- S/N 009539 --------------------------- v.04.00.04 r.0107 -
[WF] Performing Wave-Functions I/O from ./SAVE

[FFT-X] Mesh size: 15 15 15

[X-CG] R(p) Tot o/o(of R) : 2350 36720 100
[X-CG] R(p) Tot o/o(of R) : 6651 36720 100
[X-CG] R(p) Tot o/o(of R) : 6233 36720 100
[X-CG] R(p) Tot o/o(of R) : 4688 36720 100
[X-CG] R(p) Tot o/o(of R) : 8761 36720 100
[X-CG] R(p) Tot o/o(of R) : 10948 36720 100
[X-CG] R(p) Tot o/o(of R) : 9243 36720 100
[X-CG] R(p) Tot o/o(of R) : 8025 36720 100
[X-CG] R(p) Tot o/o(of R) : 9213 36720 100
[X-CG] R(p) Tot o/o(of R) : 4682 36720 100
[X-CG] R(p) Tot o/o(of R) : 6316 36720 100
[X-CG] R(p) Tot o/o(of R) : 10268 36720 100
[X-CG] R(p) Tot o/o(of R) : 8092 36720 100
[X-CG] R(p) Tot o/o(of R) : 10260 36720 100
[X-CG] R(p) Tot o/o(of R) : 10903 36720 100
[X-CG] R(p) Tot o/o(of R) : 6231 36720 100
[X-CG] R(p) Tot o/o(of R) : 6335 36720 100
[X-CG] R(p) Tot o/o(of R) : 8757 36720 100
[X-CG] R(p) Tot o/o(of R) : 6703 36720 100
[X-CG] R(p) Tot o/o(of R) : 2339 36720 100

CpuTiming [Min/Max/Average]: 45s/45s/45s

[06] Game Over & Game summary
=============================

04/11/2018 at 15:08 YAMBO @ iivrubel-mint [start]
04/11/2018 at 15:09 [end]

Timing [Min/Max/Average]: 45s/45s/45s

.-ACKNOWLEDGMENT
|
| The users of YAMBO have little formal obligations with respect to
| the YAMBO group (those specified in the GNU General Public
| License, http://www.gnu.org/copyleft/gpl.txt). However, it is
| common practice in the scientific literature, to acknowledge the
| efforts of people that have made the research possible. In this
| spirit, please find below the reference we kindly ask you to use
| in order to acknowledge YAMBO:
|
| Yambo: An ab initio tool for excited state calculations
| A. Marini, C. Hogan, M. Gr\"uning, D. Varsano
| Computer Physics Communications 180, 1392 (2009).
|

.-Input file : W1.in
| em1s # [R Xs] Static Inverse Dielectric Matrix
| BoseTemp= 0.000000 eV # Bosonic Temperature
| FFTGvecs= 949 RL # [FFT] Plane-waves
| X_Threads= 4 # [OPENMP/X] Number of threads for response functions
| DIP_Threads= 4 # [OPENMP/X] Number of threads for dipoles
| Chimod= "Hartree" # [X] IP/Hartree/ALDA/LRC/BSfxc
| % BndsRnXs
| 9 | 35 | # [Xs] Polarization function bands
| %
| NGsBlkXs= 57 RL # [Xs] Response block size
| % DmRngeXs
| 0.10000 | 0.10000 | eV # [Xs] Damping range
| %
| % LongDrXs
| 0.1000E-4 | 0.000 | 0.000 | # [Xs] [cc] Electric Field
| %
Evgeniia Cherotchenko
ITMO University, Saint-Petersburg, Russia
Evgeniia
 
Posts: 12
Joined: Mon Apr 09, 2018 2:55 pm

Re: BSE: Screened interaction matrix calculation

Postby Daniele Varsano » Wed Apr 11, 2018 1:34 pm

Dear Evgeniia,
please sign your post with your name and affiliation, This is a rule of the forum. You can fill once for all in the signature field in your profile.

The size of the matrix changes as Yambo considers the nearest number of Gvecs in your input to close Gvector shell.
Moreover, if you have already calculated the screening (i.e. it exists the ndb.em1s database in the SAVE directory) and in your input, you have a lower number of Gvecs, the database is read and the screening it is not recalculated.
About the error you get in BSE, please post your input/report/log files and we will have a look.
Please, upload your files in the post instead of copy/paste as it is easier to scroll.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

Re: BSE: Screened interaction matrix calculation

Postby Evgeniia » Wed Apr 11, 2018 3:22 pm

Dear Daniele,

1) Many thanks for your reply, I will put the files with my questions on BSE caclulation as only I prepare them in a proper way.
2) About matrix - but why then the matrix size is kept the same as NGsBlkXs for LiF and NaCl? Is it just a coincidence, or it just depends on the type of the lattice? Also, how comes, that sometimes the size of this matrix is equal to 1 after the calculation?
Sorry, I am a new yambo user, so this might be a stupid question.

Best Regards,
Evgeniia
Evgeniia Cherotchenko
ITMO University, Saint-Petersburg, Russia
Evgeniia
 
Posts: 12
Joined: Mon Apr 09, 2018 2:55 pm

Re: BSE: Screened interaction matrix calculation

Postby Daniele Varsano » Thu Apr 12, 2018 9:06 am

Dear Evgeenia,
2) About matrix - but why then the matrix size is kept the same as NGsBlkXs for LiF and NaCl? Is it just a coincidence, or it just depends on the type of the lattice? ?

The matrix size it is a parameter that has to be converged, so it is system dependent. It is set by input and as I wrote in the previous post yambo slightly the input values to close G vectors shells in order to not break the system symmetries.

Also, how comes, that sometimes the size of this matrix is equal to 1 after the calculation

This should not happen. It means that something went wrong, can you post the input and report of an example when it happens?

Sorry, I am a new yambo user, so this might be a stupid question.

Welcome in the yambo world, rarely questions are stupid.

Best,

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

Re: BSE: Screened interaction matrix calculation

Postby Evgeniia » Mon Apr 16, 2018 6:33 pm

Dear Daniele,
I am trying to implement BSE tutorial (based on LiF) to perovskite cubic cell. I faced the following problem: with the increased number of k-points in scf calculation in QE, yambo BSE stops working with netCDF error. In particular, when I take 4 4 4 net for scf, it results in 10 wave-vectors in scf folder. BSE works well in this case. Then I increase K-points in scf input to 5 5 5. Number of wave-vectors remains the same, there are 10 points, but BSE finishes with netCDF error, saying
[ERROR] STOP signal received while in :[06.04.03] Kernel loop
[ERROR][NetCDF] NetCDF: One or more variable sizes violate format constraints.

However, when I tried to repeat LiF results, the 8 8 8 net in scf calculation was fine for BSE.

I searched for this problem in general, and found that probably my yambo executive file (sorry if I use the incorrect term), was compiled in a wrong way - when I open Makefile, the netCDF option is empty, while probably it should be something like netcdf = -D_64BIT_OFFSET. If you say, that it is true, I will try to recompile everything again.

Also I could not find the Log directory at all, so I am not sure that it exists for Yambo. Could you please explain me how to make the log files, that you ask?

I attach the archive,with my outputs, inputs, in .txt format if it makes sense. Also I copied the command line from yambo initialization to BSE run to the text file.

That would be great, if you help me to figure out, why nothing works)
Best Regards,
Evgeniia
You do not have the required permissions to view the files attached to this post.
Evgeniia Cherotchenko
ITMO University, Saint-Petersburg, Russia
Evgeniia
 
Posts: 12
Joined: Mon Apr 09, 2018 2:55 pm

Re: BSE: Screened interaction matrix calculation

Postby Daniele Varsano » Mon Apr 16, 2018 7:07 pm

Dear Eugenvia,
I do not think you have problems with netcdf libraries, as you are able to run yambo in the system of the tutorial, and read and write databases. Usually, NetCDF errors are just fingerprint of other errors occurring beacuase of some incosistent input prameters, bad parallelization strategy etc.

In your case the problem is your choice of the BSEbands, you have a semiconductor with 36 electrons:
Code: Select all
States summary         : Full        Metallic    Empty
                           0001-0018               0019-0035

where the last occupied bands is the band number 18 and the first unoccupied is the 19th.
In your BSEbands you are including occupied bands only, so no transitions (electron-hole) are possible with the current choice, so Yambo cannot build the excitonic matrix.
Code: Select all
%BSEBands
10|14|                       #  (BSK)   Bands range
%


I've also noticed that you have compiled Yambo in serial only with OpenMP support, this is the reason you do not have the LOG directory, you should have a log file in your main directory. If you do not have it is because you run the code interactively so the log is printed to the standard output.
I strongly suggest you compile the code using MPI otherwise calculations with converged parameters will be very slow and memory consuming.
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

Re: BSE: Screened interaction matrix calculation

Postby Evgeniia » Thu Apr 19, 2018 12:13 pm

Dear Daniele,

At first, many thanks for you reply. Unfortunately now there is no option to compile Yambo with MPI, so with this computer I will test only small systems, and large calculations will be done with the help of university computer center.

I tried to change my bse zones, (indeed that was my stupid mistake), if last occupied band is 18, so I took the range from 16th to 22. However the error was the same - [ERROR] STOP signal received while in :[06.04.03] Kernel loop
[ERROR][NetCDF] NetCDF: One or more variable sizes violate format constraints.


Now I am trying zones form 1 to 35, however I think the result will be similar...
At the same time I double checked calculation for K-points 444 000 is scf, and BSE worked.

Best Regards,
Evgeniia
Evgeniia Cherotchenko
ITMO University, Saint-Petersburg, Russia
Evgeniia
 
Posts: 12
Joined: Mon Apr 09, 2018 2:55 pm

Re: BSE: Screened interaction matrix calculation

Postby Daniele Varsano » Thu Apr 19, 2018 12:33 pm

Dear Evgeniia,
can you post input, report and log file?

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

Re: BSE: Screened interaction matrix calculation

Postby Evgeniia » Thu Apr 19, 2018 12:52 pm

Dear Daniele,

May I ask again, what command should I use to create the log file in the main directory? And when should I do it (after the BSE calc)?

Best Regards
Evgeniia
Evgeniia Cherotchenko
ITMO University, Saint-Petersburg, Russia
Evgeniia
 
Posts: 12
Joined: Mon Apr 09, 2018 2:55 pm

Re: BSE: Screened interaction matrix calculation

Postby Daniele Varsano » Thu Apr 19, 2018 1:34 pm

Dear Evgeniia,
the log files is generated automatically when you run in batch, if you are running in interactive mode just redirect your standard output
> yamgo -F file.in > log

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

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