Hello,
In the ndb.dipoles dataset, the DIP_v only contains the off-diagonal matrix elements (i.e., <c|v^\hat|v>). Is it possible to calculate the diagonal matrix elements, i.e. <n|v^\hat|n>, n is any KS state and v^\hat is the velocity operator?
Best,
Xiaoming
diagonal matrix elements of the velocity operator
Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, andrea marini, Daniele Varsano, Conor Hogan
-
Xiaoming Wang
- Posts: 67
- Joined: Fri Dec 18, 2020 7:14 am
diagonal matrix elements of the velocity operator
Xiaoming Wang
The University of Toledo
The University of Toledo
-
Daniele Varsano
- Posts: 3810
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: diagonal matrix elements of the velocity operator
Dear Xiamong,
uncommenting the variable #DipBandsALL yambo will calculate all the dipoles matrix elements.
the variables appears building the input as:
./yambo -dipoles -V all
Best,
Daniele
uncommenting the variable #DipBandsALL yambo will calculate all the dipoles matrix elements.
the variables appears building the input as:
./yambo -dipoles -V all
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/
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/
-
Xiaoming Wang
- Posts: 67
- Joined: Fri Dec 18, 2020 7:14 am
Re: diagonal matrix elements of the velocity operator
Thanks Daniele, it works but some strange behavior results. I have 576 kpts (12*12*4), the first 44 kpts data are missing for DIP_v but not for DIP_iR.
E.g. using ncdump -v DIP_v ndb.dipoles, I got something like
What's the possible reason of that?
Best,
Xiaoming
E.g. using ncdump -v DIP_v ndb.dipoles, I got something like
Code: Select all
netcdf ndb {
dimensions:
D_0000000003 = 3 ;
D_0000000001 = 1 ;
D_0000000002 = 2 ;
D_0000000004 = 4 ;
D_0000000011 = 11 ;
D_0000000100 = 100 ;
D_0000000032 = 32 ;
D_0000000008 = 8 ;
D_0000000576 = 576 ;
variables:
float HEAD_VERSION(D_0000000003) ;
float HEAD_REVISION(D_0000000001) ;
float SERIAL_NUMBER(D_0000000001) ;
float SPIN_VARS(D_0000000002) ;
float HEAD_R_LATT(D_0000000004) ;
float HEAD_WF(D_0000000001) ;
float FRAGMENTED(D_0000000001) ;
float TEMPERATURES(D_0000000002) ;
float PARS(D_0000000011) ;
char APPROACH(D_0000000001, D_0000000100) ;
char KINDS(D_0000000001, D_0000000100) ;
char WAVE_FUNC_XC(D_0000000001, D_0000000100) ;
float DIP_iR(D_0000000001, D_0000000576, D_0000000008, D_0000000032, D_0000000003, D_0000000002) ;
float DIP_P(D_0000000001, D_0000000576, D_0000000008, D_0000000032, D_0000000003, D_0000000002) ;
float DIP_v(D_0000000001, D_0000000576, D_0000000008, D_0000000032, D_0000000003, D_0000000002) ;
data:
DIP_v =
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
_, _,
Best,
Xiaoming
Xiaoming Wang
The University of Toledo
The University of Toledo
-
Xiaoming Wang
- Posts: 67
- Joined: Fri Dec 18, 2020 7:14 am
Re: diagonal matrix elements of the velocity operator
Here is my report file
Code: Select all
/$$ /$$ /$$$$$$ /$$ /$$ /$$$$$$$ /$$$$$$
| $$ /$$//$$__ $$| $$$ /$$$| $$__ $$ /$$__ $$
\ $$ /$$/| $$ \ $$| $$$$ /$$$$| $$ \ $$| $$ \ $$
\ $$$$/ | $$$$$$$$| $$ $$/$$ $$| $$$$$$$ | $$ | $$
\ $$/ | $$__ $$| $$ $$$| $$| $$__ $$| $$ | $$
| $$ | $$ | $$| $$\ $ | $$| $$ \ $$| $$ | $$
| $$ | $$ | $$| $$ \/ | $$| $$$$$$$/| $$$$$$/
|__/ |__/ |__/|__/ |__/|_______/ \______/
Version 5.0.3 Revision 19584 Hash 1cce2ba63
Branch is
MPI+OpenMP+SLK+SLEPC+HDF5_MPI_IO Build
http://www.yambo-code.org
08/11/2021 at 11:33 yambo @ r1i6n31
==================================================
Cores-Threads : 36(CPU)-1(threads)
MPI Cores : 36
Threads per core : 1
Threads total : 36
Nodes Computing : 1
Nodes IO : 1
Fragmented WFs : yes
CORE databases : .
Additional I/O : .
Communications : .
Input file : optics.in
Report file : ./r_optics_dipoles_02
Verbose log/report : no
Log files : ./LOG
Precision : SINGLE
[RD./SAVE//ns.db1]--------------------------------------------------------------
Bands : 40
K-points : 576
G-vectors : 21171 [RL space]
Components : 2695 [wavefunctions]
Symmetries : 1 [spatial]
Spinor components : 1
Spin polarizations : 1
Temperature : 0.000000 [eV]
Electrons : 16.00000
WF G-vectors : 4073
Max atoms/species : 2
No. of atom species : 2
Exact exchange fraction in XC : 0.000000
Exact exchange screening in XC : 0.000000
Magnetic symmetries : no
- S/N 002115 ---------------------------------------------- v.05.00.03 r.19584 -
[02] CORE Variables Setup
=========================
[02.01] Unit cells
==================
Cell kind : HCP
Atoms in the cell : B N
number of B atoms : 2
number of N atoms : 2
Alat factors : 4.72809 4.09465 12.50432 [a.u.]
Direct lattice volume : 242.0823 [a.u.]
Direct lattice vectors: A[ 1 ] A[ 2 ] A[ 3 ]
A[ 1 ]: 1.000000 0.000000 0.000000 [iru]
A[ 2 ]: -0.500000 1.000000 0.000000 [iru]
A[ 3 ]: 0.000000 0.000000 1.000000 [iru]
Recip. lattice volume : 1.024653 [a.u.]
Recip. lattice vectors: B[ 1 ] B[ 2 ] B[ 3 ]
B[ 1 ]: 1.000000 0.500000 0.000000 [iku]
B[ 2 ]: 0.000000 1.000000 0.000000 [iku]
B[ 3 ]: 0.000000 0.000000 1.000000 [iku]
[02.02] Symmetries
==================
Inversion symmetry : no
Spatial inversion : no
K-space Time-reversal : no
Magnetic symmetries : no
Group table correct : yes
Symmetries units : [cc]
[S 1]: 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000
[02.03] Reciprocal space
========================
nG shells : 1116
nG charge : 21171
nG WFs : 4073
nC WFs : 2695
G-vecs. in first 80 shells: [ Number ]
1 3 5 7 13 25 37 39 51
53 65 71 83 95 107 109 121 127
139 151 163 175 187 189 201 213 225
237 249 251 263 287 311 323 335 359
371 373 397 403 415 427 439 463 475
487 499 511 513 537 549 561 573 585
591 603 627 639 651 663 675 677 689
713 737 749 761 785 809 821 833 845
869 881 883 907 931 943 955 967
...
Shell energy in first 80 shells: [ mHa ]
0.00000 126.244 504.975 1136.19 1177.32 1303.57 1682.30 2019.90 2313.52
3156.09 3197.22 3531.97 3658.22 4036.95 4333.42 4544.77 4668.17 4709.30
4835.54 5214.27 5551.87 5722.10 5845.49 6185.94 6688.07 6729.20 7363.27
7865.39 8076.75 8079.60 8241.27 8367.51 8746.25 9254.07 9256.92 9377.46
9717.92 10225.7 10261.2 10595.9 10722.2 10895.2 11100.9 11397.4 11403.1
11611.6 11732.1 12615.8 12624.4 12786.0 12788.9 13752.0 13757.7 13801.7
14127.9 14254.1 14427.2 14632.9 14935.0 15140.7 15264.1 15275.5 15305.2
15431.5 15810.2 16147.8 16156.3 16320.9 16441.4 16452.8 16781.9 17284.0
17325.1 17333.7 18179.1 18461.3 18467.0 18672.7 18675.5 18807.5
...
[02.04] K-grid lattice
======================
Compatible Grid is : 3D
Base K vectors : K_min[ 1 ] K_min[ 2 ] K_min[ 3 ]
K_min[ 1 ] : -0.833333E-1 -0.745058E-8 0.00000 [rlu]
K_min[ 2 ] : 0.000000 0.083333 0.000000 [rlu]
K_min[ 3 ] : 0.000000 0.000000 0.250000 [rlu]
Grid dimensions : 12 12 4
K lattice UC volume : 0.001779 [a.u.]
[02.05] Energies & Occupations
==============================
[X] === General ===
[X] Electronic Temperature : 0.000000 0.000000 [eV K]
[X] Bosonic Temperature : 0.000000 0.000000 [eV K]
[X] Finite Temperature mode : no
[X] El. density : 0.44602E+24 [cm-3]
[X] Fermi Level : 4.782450 [eV]
[X] === Gaps and Widths ===
[X] Conduction Band Min : 4.308568 [eV]
[X] Valence Band Max : 0.000000 [eV]
[X] Filled Bands : 8
[X] Empty Bands : 9 40
[X] Direct Gap : 4.673592 [eV]
[X] Direct Gap localized at k-point : 211
[X] Indirect Gap : 4.308568 [eV]
[X] Indirect Gap between k-points : 211 25
[X] Last valence band width : 3.198007 [eV]
[X] 1st conduction band width : 4.079237 [eV]
[03] Transferred momenta grid and indexing
==========================================
[RD./SAVE//ndb.kindx]-----------------------------------------------------------
Fragmentation : no
Polarization last K : 576
QP states : 1 576
X grid is uniform : yes
Grids : X B S
*ERR*BS scattering : yes
COLL scattering : no
Sigma scattering : yes
X scattering : yes
- S/N 002115 ---------------------------------------------- v.05.00.03 r.19584 -
[BZ sampling] Q-grid is User defined and/or read from the database
IBZ Q-points : 576
BZ Q-points : 576
K/Q-points units:
rlu = crystal or reduced units; cc = cartesian coordinates; iku = interal k-units
Q [ 1]: 0.000000 0.000000 0.000000 [rlu]
Q [ 2]: 0.000000 0.000000 0.250000 [rlu]
Q [ 3]: 0.000000 0.000000 -0.500000 [rlu]
Q [ 4]: 0.000000 0.000000 -0.250000 [rlu]
Q [ 5]: 0.000000 0.083333 0.000000 [rlu]
Q [ 6]: 0.000000 0.083333 0.250000 [rlu]
Q [ 7]: 0.000000 0.083333 -0.500000 [rlu]
Q [ 8]: 0.000000 0.083333 -0.250000 [rlu]
Q [ 9]: 0.000000 0.166667 0.000000 [rlu]
Q [ 10]: 0.000000 0.166667 0.250000 [rlu]
Q [ 11]: 0.000000 0.166667 -0.500000 [rlu]
Q [ 12]: 0.000000 0.166667 -0.250000 [rlu]
Q [ 13]: 0.000000 0.250000 0.000000 [rlu]
Q [ 14]: 0.000000 0.250000 0.250000 [rlu]
Q [ 15]: 0.000000 0.250000 -0.500000 [rlu]
Q [ 16]: 0.000000 0.250000 -0.250000 [rlu]
Q [ 17]: 0.000000 0.333333 0.000000 [rlu]
Q [ 18]: 0.000000 0.333333 0.250000 [rlu]
Q [ 19]: 0.000000 0.333333 -0.500000 [rlu]
Q [ 20]: 0.000000 0.333333 -0.250000 [rlu]
Q [ 21]: 0.000000 0.416667 0.000000 [rlu]
Q [ 22]: 0.000000 0.416667 0.250000 [rlu]
Q [ 23]: 0.000000 0.416667 -0.500000 [rlu]
Q [ 24]: 0.000000 0.416667 -0.250000 [rlu]
Q [ 25]: 0.000000 -0.500000 0.000000 [rlu]
Q [ 26]: 0.000000 -0.500000 0.250000 [rlu]
Q [ 27]: 0.000000 -0.500000 -0.500000 [rlu]
Q [ 28]: 0.000000 -0.500000 -0.250000 [rlu]
Q [ 29]: 0.000000 -0.416667 0.000000 [rlu]
Q [ 30]: 0.000000 -0.416667 0.250000 [rlu]
Q [ 31]: 0.000000 -0.416667 -0.500000 [rlu]
Q [ 32]: 0.000000 -0.416667 -0.250000 [rlu]
Q [ 33]: 0.000000 -0.333333 0.000000 [rlu]
Q [ 34]: 0.000000 -0.333333 0.250000 [rlu]
Q [ 35]: 0.000000 -0.333333 -0.500000 [rlu]
Q [ 36]: 0.000000 -0.333333 -0.250000 [rlu]
Q [ 37]: 0.000000 -0.250000 0.000000 [rlu]
Q [ 38]: 0.000000 -0.250000 0.250000 [rlu]
Q [ 39]: 0.000000 -0.250000 -0.500000 [rlu]
Q [ 40]: 0.000000 -0.250000 -0.250000 [rlu]
Q [ 41]: 0.000000 -0.166667 0.000000 [rlu]
Q [ 42]: 0.000000 -0.166667 0.250000 [rlu]
Q [ 43]: 0.000000 -0.166667 -0.500000 [rlu]
Q [ 44]: 0.000000 -0.166667 -0.250000 [rlu]
Q [ 45]: 0.000000 -0.083333 0.000000 [rlu]
Q [ 46]: 0.000000 -0.083333 0.250000 [rlu]
Q [ 47]: 0.000000 -0.083333 -0.500000 [rlu]
Q [ 48]: 0.000000 -0.083333 -0.250000 [rlu]
Q [ 49]: 0.833333E-1 0.745058E-8 0.00000 [rlu]
Q [ 50]: 0.833333E-1 0.745058E-8 0.250000 [rlu]
Remaining 526 points informations can be written running with -fatlog
[03.01] X indexes
=================
[03.01.01] Sigma indexes
========================
[WR./SAVE//ndb.kindx]-----------------------------------------------------------
Fragmentation : no
Polarization last K : 576
QP states : 1 576
X grid is uniform : yes
Grids : X S
BS scattering : no
COLL scattering : no
Sigma scattering : yes
X scattering : yes
- S/N 002115 ---------------------------------------------- v.05.00.03 r.19584 -
[04] Dipoles
============
[WARNING] DIPOLES database not correct or missing
[RD./SAVE//ns.kb_pp_pwscf]------------------------------------------------------
Fragmentation : yes
- S/N 002115 ---------------------------------------------- v.05.00.03 r.19584 -
[WF-Oscillators/G space/Transverse up loader] Normalization (few states) min/max : 0.000000 1.000000
[WR./SAVE//ndb.dipoles]---------------------------------------------------------
Brillouin Zone Q/K grids (IBZ/BZ) : 576 576 576 576
RL vectors : 4077 [WF]
Fragmentation : yes
Electronic Temperature : 0.000000 [K]
Bosonic Temperature : 0.000000 [K]
DIP band range : 1 40
DIP band range limits : 40 1
DIP e/h energy range : -1.000000 -1.000000 [eV]
RL vectors in the sum : 4077
[r,Vnl] included : yes
Bands ordered : no
Direct v evaluation : no
Approach used : G-space v
Dipoles computed : R V P
Wavefunctions : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
- S/N 002115 ---------------------------------------------- v.05.00.03 r.19584 -
[WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
[WARNING] In case H contains other non local terms, these are neglected
Timing [Min/Max/Average]: 42s/42s/42s
[05] Timing Overview
====================
Clock: global (MAX - min (if any spread is present) clocks)
io_ATMPROJ_pwscf : 0.0030s P21 [MAX] 0.0000s P4 [min]
IO_and_Messaging_switch : 0.0024s P26 (388 calls, 0.006 msec avg) [MAX] 0.0000s P16 ( 4 calls, 0.005 msec avg) [min]
io_KB_abinit : 0.0004s P33 [MAX] 0.0000s P35 [min]
io_Double_Grid : 0.0005s P3 [MAX] 0.0001s P32 [min]
io_BS : 0.0030s P4 [MAX] 0.0001s P28 [min]
io_COL_CUT : 0.0005s P12 [MAX] 0.0003s P2 [min]
io_HF : 0.0010s P2 [MAX] 0.0006s P20 [min]
io_X : 0.0020s P4 ( 4 calls, 0.500 msec avg) [MAX] 0.0009s P2 ( 4 calls, 0.236 msec avg) [min]
io_fragment : 16.1635s P36 (768 calls, 0.021 msec avg) [MAX] 0.0016s P29 [min]
PP_uspp_init : 0.0190s P33 (192 calls, 0.099 msec avg) [MAX] 0.0056s P10 (192 calls, 0.029 msec avg) [min]
DIPOLE_transverse : 41.7091s P33 [MAX] 0.0229s P30 [min]
io_WF : 11.3757s P12 (577 calls, 0.020 msec avg) [MAX] 0.0284s P30 [min]
io_KB_pwscf : 20.1779s P27 (578 calls, 0.035 msec avg) [MAX] 0.0633s P30 ( 3 calls, 21.099 msec avg) [min]
io_GROT : 0.0806s P2 ( 3 calls, 26.861 msec avg) [MAX] 0.0790s P17 ( 3 calls, 26.328 msec avg) [min]
io_QINDX : 0.1374s P1 ( 3 calls, 45.785 msec avg) [MAX] 0.1051s P7 ( 3 calls, 35.033 msec avg) [min]
bz_samp_indexes : 0.1075s P7 [MAX] 0.1051s P2 [min]
io_DIPOLES : 0.6986s P1 (197 calls, 3.546 msec avg) [MAX] 0.2946s P3 ( 5 calls, 58.925 msec avg) [min]
WF_load_FFT : 10.7566s P12 (192 calls, 0.056 msec avg) [MAX] 0.6056s P34 (192 calls, 3.154 msec avg) [min]
Dipoles : 42.8304s P34 [MAX] 42.8303s P26 [min]
[06] Memory Overview
====================
Memory Usage: global (Only MASTER cpu here). [O] stands for group 'O'
Memory treshold are: 73.31400 [Mb] (basic treshold) 733.1400 [Mb] (SAVEs treshold)
Max memory used : 135.3400 [Mb]
[07] Game Over & Game summary
=============================
08/11/2021 at 11:33 yambo @ r1i6n31 [start]
08/11/2021 at 11:34 [end]
Timing [Min/Max/Average]: 44s/44s/44s
[Time-Profile]: 44s
.-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
|
| Many-body perturbation theory calculations using the yambo code
| D. Sangalli, A. Ferretti, H. Miranda, C. Attaccalite, I. Marri, E. Cannuccia, P. Melo,
| M Marsili, F Paleari, A Marrazzo, G Prandini, P Bonfà, M O Atambo, F Affinito,
| M Palummo, A Molina-Sánchez, C Hogan, M Grüning, D Varsano and A Marini.
| J. Phys.: Condens. Matter 31, 325902 (2019).
|
| Yambo: An ab initio tool for excited state calculations
| A. Marini, C. Hogan, M. Grüning, D. Varsano
| Computer Physics Communications 180, 1392 (2009).
|
.-Input file optics.in
| optics # [R] Linear Response optical properties
| dipoles # [R] Oscillator strenghts (or dipoles)
| BoseTemp= 0.000000 eV # Bosonic Temperature
| NLogCPUs= 1 # [PARALLEL] Live-timing CPU`s (0 for all)
| DIP_CPU= "6.2.3" # [PARALLEL] CPUs for each role
| DIP_ROLEs= "v.c.k" # [PARALLEL] CPUs roles (k,c,v)
| DIP_Threads= 1 # [OPENMP/X] Number of threads for dipoles
| X_Threads=0 # [OPENMP/X] Number of threads for response functions
| DipBandsALL # [DIP] Compute all bands range, not only valence and conduction
| DipComputed= "R V P" # [DIP] [default R P V; extra P2 Spin Orb]
Xiaoming Wang
The University of Toledo
The University of Toledo
-
Xiaoming Wang
- Posts: 67
- Joined: Fri Dec 18, 2020 7:14 am
Re: diagonal matrix elements of the velocity operator
Not sure if it is a bug. For my system, the not complete or none written of DIP_v is due to the parallelism over conduction or valence bands used. Parallel over kpoint only solve the problem.
Best,
Xiaoming
Best,
Xiaoming
Xiaoming Wang
The University of Toledo
The University of Toledo
-
Xiaoming Wang
- Posts: 67
- Joined: Fri Dec 18, 2020 7:14 am
Re: diagonal matrix elements of the velocity operator
Hello,
I'm wondering if the problem for band parallelization can be solved? Since my system has fewer k points but lots of bands.
Best,
Xiaoming
I'm wondering if the problem for band parallelization can be solved? Since my system has fewer k points but lots of bands.
Best,
Xiaoming
Xiaoming Wang
The University of Toledo
The University of Toledo
-
Daniele Varsano
- Posts: 3810
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: diagonal matrix elements of the velocity operator
Dear Xiaoming,
thanks for reporting, sorry I have overlooked this. We will have a look asap.
Best,
Daniele
thanks for reporting, sorry I have overlooked this. We will have a look asap.
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/
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/