ver3.3.0-excitons wave plot:without output files

[hbshu]

Dear all:
I have finished my BSE calculation ( yambo -b -o b -y d). After that, I want to have an exciton wave to plot by ypp -e w and it show the following information without any output files. what's the problem and how to resolve it???? Thanks!

[01] Y(ambo) P(ost)/(re) P(rocessor)
29 <---> [02] Core DB
30 <---> :: Electrons : 44.00000
31 <---> :: Temperature [ev]: 0.000000
32 <---> :: Lattice factors [a.u.]: 24.94439 25.51130 10.01776
33 <---> :: K points : 13
34 <---> :: Bands : 400
35 <---> :: Symmetries : 2
36 <---> :: RL vectors : 400283
37 <---> [03] K-point grid
38 <---> :: Q-points (IBZ): 13
39 <---> :: X K-points (IBZ): 13
40 <---> [04] CORE Variables Setup
41 <---> [04.01] Unit cells
42 <---> [04.02] Symmetries
43 <---> [04.03] RL shells
44 <---> [04.04] K-grid lattice
45 <---> [04.05] Energies [ev] & Occupations
46 <---> [05] Game Over
~
~the ypp.in is as followed:

9 # GPL Version 3.3.0 Revision 1887
10 # http://www.yambo-code.org
11 #
12 wavefunction # [R] Wavefunction
13 excitons # [R] Excitons
14 Format= "c" # Output format [(c)ube/(g)nuplot/(x)crysden]
15 Direction= "3" # [rlu] [1/2/3] for 1d or [12/13/23] for 2d [123] for 3D
16 FFTGvecs= 55911 RL # [FFT] Plane-waves
17 States= "1 - 1" # Index of the BS state(s)
18 Degen_Step= 0.0100 eV # Maximum energy separation of two degenerate states
19 % Cells
20 1 | 1 | 5 | # Number of cell repetitions (even or 1)
21 %
22 % Hole
23 0.00 | 0.00 | 0.00 | # [cc] Hole position in unit cell
24 %

the bse.in is as followed:
1 # ____ ____ _ ____ ____ ______ ___
2 # |_ _||_ _| / \ |_ \ / _||_ _ \ ." `.
3 # \ \ / / / _ \ | \/ | | |_) | / .-. \
4 # \ \/ / / ___ \ | |\ /| | | __". | | | |
5 # _| |_ _/ / \ \_ _| |_\/_| |_ _| |__) |\ `-" /
6 # |______||____| |____||_____||_____||_______/ `.___."
7 #
8 # GPL Version 3.3.0 Revision 1887
9 # http://www.yambo-code.org
10 #
11 rim_cut # [R RIM CUT] Coulomb interaction
12 em1s # [R Xs] Static Inverse Dielectric Matrix
13 optics # [R OPT] Optics
14 bse # [R BSK] Bethe Salpeter Equation.
15 bss # [R BSS] Bethe Salpeter Equation solver
16 StdoHash= 20 # [IO] Live-timing Hashes
17 Nelectro= 44.00000 # Electrons number
18 ElecTemp= 0.000000 eV # Electronic Temperature
19 BoseTemp=0.000000 eV # Bosonic Temperature
20 OccTresh=0.1000E-4 # Occupation treshold (metallic bands)
21 FFTGvecs= 55911 RL # [FFT] Plane-waves
22 NonPDirs= "XY" # [X/BSS] Non periodic chartesian directions (X,Y,Z,XY...)
23 RandQpts=1000000 # [RIM] Number of random q-points in the BZ
24 RandGvec=1 RL # [RIM] Coulomb interaction RS components
25 #QpgFull # [F RIM] Coulomb interaction: Full matrix
26 % Em1Anys
27 0.00 | 0.00 | 0.00 | # [RIM] X Y Z Static Inverse dielectric matrix
28 %
29 IDEm1Ref=0 # [RIM] Dielectric matrix reference component 1(x)/2(y)/3(z)
30 CUTGeo= "box xy" # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere
31 % CUTBox
32 12.47219 | 12.75565 | 0.00000 | # [CUT] [au] Box sides
33 %
34 CUTRadius= 0.000000 # [CUT] [au] Sphere/Cylinder radius
35 CUTCylLen= 0.000000 # [CUT] [au] Cylinder length
36 #CUTCol_test # [CUT] Perform a cutoff test in R-space
37 KfnQPdb= "E < GW-Z/db.QP" # [EXTQP BSK BSS] Database
38 KfnQP_N= 1 # [EXTQP BSK BSS] Interpolation neighbours
39 % KfnQP_E
40 0.000000 | 1.000000 | 1.000000 | # [EXTQP BSK BSS] E parameters (c/v) eV|adim|adim
41 %
42 % KfnQP_Wv
43 0.00 | 0.00 | 0.00 | # [EXTQP BSK BSS] W parameters (valence) eV|adim|eV^-1
44 %
45 % KfnQP_Wc
46 0.00 | 0.00 | 0.00 | # [EXTQP BSK BSS] W parameters (conduction) eV|adim|eV^-1
47 %
48 KfnQP_Z= ( 1.000000 , 0.000000 ) # [EXTQP BSK BSS] Z factor (c/v)
49 BSresKmod= "xc" # [BSK] Resonant Kernel mode. (`x`;`c`;`d`)
50 BScplKmod= "none" # [BSK] Coupling Kernel mode. (`x`;`c`;`d`)
51 % BSEBands
52 10 | 30 | # [BSK] Bands range
53 %
54 BSENGBlk= 6 Ry # [BSK] Screened interaction block size
55 BSENGexx= 55911 RL # [BSK] Exchange components
56 #ALLGexx # [BSS] Force the use use all RL vectors for the exchange part
57 % BSEEhEny
58 -5.000000 |6.000000 | eV # [BSK] Electron-hole energy range
59 %
60 XfnQPdb= "none" # [EXTQP Xd] Database
61 XfnQP_N= 1 # [EXTQP Xd] Interpolation neighbours
62 % XfnQP_E
63 0.000000 | 1.000000 | 1.000000 | # [EXTQP Xd] E parameters (c/v) eV|adim|adim
64 %
65 % XfnQP_Wv
66 0.00 | 0.00 | 0.00 | # [EXTQP Xd] W parameters (valence) eV|adim|eV^-1
67 %
68 % XfnQP_Wc
69 0.00 | 0.00 | 0.00 | # [EXTQP Xd] W parameters (conduction) eV|adim|eV^-1
70 %
71 XfnQP_Z= ( 1.000000 , 0.000000 ) # [EXTQP Xd] Z factor (c/v)
72 % QpntsRXs
73 1 | 13 | # [Xs] Transferred momenta
74 %
75 % BndsRnXs
76 1 | 320 | # [Xs] Polarization function bands
77 %
78 NGsBlkXs= 6 Ry # [Xs] Response block size
79 CGrdSpXs= 100.0000 # [Xs] [o/o] Coarse grid controller
80 % EhEngyXs
81 -5.000000 |6.000000 | eV # [Xs] Electron-hole energy range
82 %
83 % LongDrXs
84 0.000000 | 0.000000 | 1.000000 | # [Xs] [cc] Electric Field
85 %
86 DrudeWXs= ( 0.00 , 0.00 ) eV # [Xs] Drude plasmon
87 BoseCut= 0.10000 # [BOSE] Finite T Bose function cutoff
88 BSSmod= "d" # [BSS] Solvers `h/d/i/t`
89 % BEnRange
90 0.00000 | 10.00000 | eV # [BSS] Energy range
91 %
92 % BDmRange
93 0.10000 | 0.10000 | eV # [BSS] Damping range
94 %
95 BEnSteps= 200 # [BSS] Energy steps
96 % BLongDir
97 0.000000 | 0.000000 | 1.000000 | # [BSS] [cc] Electric Field
98 %
99 WRbsWF # [BSS] Write to disk excitonic the FWs
-------------------------------------------------------------------------------------
the report file of BSE 1 __ __ _ __ __ ____ U ___ u
2 \ \ / / U /"\ U u |" \/ "| u U | __") u \/"_ \/
3 \ V / \/ _ \/ \| |\/| |/ \| _ \/ | | | |
4 U_|"|_u / ___ \ | | | | | |_) | .-,_| |_| |
5 |_| /_/ \_\ |_| |_| |____/ \_)-\___/
6 .-,//|(_ \\ >> <<,-,,-. _|| \\_ \\
7 \_) (__) (__) (__) (./ \.) (__) (__) (__)
8
9 GPL Version 3.3.0 Revision 1887
10 http://www.yambo-code.org
11
12 YAMBO@n69 x 008 CPUs * 06/27/2013 08:32
13
14 [01] Files & I/O Directories
15 ============================
16
17 ** Distributed Memory Run **
18
19 CORE databases in .
20 Additional I/O in .
21 Communications in .
22 Input file is bse.in
23 Report file is ./r-BES_optics_bse_em1s_bss_rim_cut
24 Job string is BES
25 Log file is ./l-BES_optics_bse_em1s_bss_rim_cut
26
27 [RD./SAVE//s.db1]-------------------------------------------
28 Bands : 400
29 K-points : 13
30 G-vectors [RL space]: 400283
31 Components [wavefunctions]: 50089
32 Symmetries [spatial+T-rev]: 2
33 Spinor components : 1
34 Spin polarizations : 1
35 Temperature [ev]: 0.000000
36 Electrons : 44.00000
37 WF G-vectors : 55911
38 Max atoms/species : 8
39 No. of atom species : 3
40 Magnetic symmetries : no
41 - S/N 008408 --------------------------- v.03.03.00 r.1887 -
42
43 [02] CORE Variables Setup
44 =========================
45
46
47 [02.01] Unit cells
48 ==================
49
50 Unit cell is Unknown
51
52 ... containing 2Mo4S8H atoms
53
54 ... with scaling factors [a.u.]: 24.94439 25.51130 10.01776
55
1,7 Top
844 | Computer Physics Communications 180, 1392 (2009).
845 |
846
847 .-Input file : bse.in
848 | optics # [R OPT] Optics
849 | bse # [R BSK] Bethe Salpeter Equation.
850 | em1s # [R Xs] Static Inverse Dielectric Matrix
851 | bss # [R BSS] Bethe Salpeter Equation solver
852 | rim_cut # [R RIM CUT] Coulomb interaction
853 | BoseTemp= 0.000000 eV # Bosonic Temperature
854 | NonPDirs= "XY" # [X/BSS] Non periodic chartesian directions (X,Y,Z,XY...)
855 | RandQpts= 1000000 # [RIM] Number of random q-points in the BZ
856 | RandGvec= 1 RL # [RIM] Coulomb interaction RS components
857 | CUTGeo= "box xy" # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere
858 | % CUTBox
859 | 12.47219 | 12.75565 | 0.00000 | # [CUT] [au] Box sides
860 | %
861 | CUTRadius= 0.000000 # [CUT] [au] Sphere/Cylinder radius
862 | CUTCylLen= 0.000000 # [CUT] [au] Cylinder length
863 | KfnQPdb= "E < GW-Z/db.QP" # [EXTQP BSK BSS] Database
864 | BSresKmod= "xc" # [BSK] Resonant Kernel mode. (`x`;`c`;`d`)
865 | BScplKmod= "none" # [BSK] Coupling Kernel mode. (`x`;`c`;`d`)
866 | % BSEBands
867 | 10 | 30 | # [BSK] Bands range
868 | %
869 | BSENGBlk= 6 Ry # [BSK] Screened interaction block size
870 | BSENGexx= 55911 RL # [BSK] Exchange components
871 | % BSEEhEny
872 | -5.000000 | 6.000000 | eV # [BSK] Electron-hole energy range
873 | %
874 | % QpntsRXs
875 | 1 | 13 | # [Xs] Transferred momenta
876 | %
877 | % BndsRnXs
878 | 1 | 320 | # [Xs] Polarization function bands
879 | %
880 | NGsBlkXs= 6 Ry # [Xs] Response block size
881 | % EhEngyXs
882 | -5.000000 | 6.000000 | eV # [Xs] Electron-hole energy range
883 | %
884 | % LongDrXs
885 | 0.000 | 0.000 |0.1000E-4 | # [Xs] [cc] Electric Field
886 | %
887 | BSSmod= "d" # [BSS] Solvers `h/d/i/t`
888 | % BEnRange
889 | 0.00000 | 10.00000 | eV # [BSS] Energy range
890 | %
891 | % BDmRange
892 | 0.10000 | 0.10000 | eV # [BSS] Damping range
893 | %
894 | BEnSteps= 200 # [BSS] Energy steps
895 | % BLongDir
896 | 0.000 | 0.000 |0.1000E-4 | # [BSS] [cc] Electric Field
897 | %
898 | WRbsWF # [BSS] Write to disk excitonic the FWs
----------------------------------------------------------------------------------
hbshu Department of physics southeast university in china

[Daniele Varsano]

Dear Hbshu,
if you want a cube file, this is a 3D plot and you should put:

Code: Select all

 Direction= "123" # [rlu] [1/2/3] for 1d or [12/13/23] for 2d [123] for 3D

Anyway, I'm not sure that this is the reason, yambo is not calculating the excitonic wavefunction.
Try to change your direction keyword, or try before a 1d plot, for instance in gnuplot form. If this
is not working, post us your input/report files of the BSE calculation and the ypp.in. Please post
them as attachement and not pasted in the post, as now some part of the report is missing and it is
not easy to read.

Best,

Daniele

[hbshu]

Dear Daniele:
thanks!

[hbshu]

Dear :
my input/report files of the BSE calculation are following:

bse.txt

[Daniele Varsano]

Dear Hbhsu,
the attachment are missing, please check if you uploaded it correctly.

Daniele

[hbshu]

Dear :
why upload attachment only one is accepted? warning:"Sorry, the board attachment quota has been reached."

[Daniele Varsano]

Thanks hbshu,
we will have a look to this issue.
Daniele

[Daniele Varsano]

Dear Hbhsu,
the attachment quota has been increased. Try to upload them now. I suggest you to compress all the files you want to upload in just one file using tar or zip.

Best,

Daniele

[hbshu]

Dear Daniele:
'ypp -e s and ypp -e a ' is correct, when ploting the excitonic wave-function by 'ypp -e w' ,a question is occuring ,the folling down:'Segmentation fault'

----------------------------------------------------------------------------------------------
__ _______ __ __ _______ _______
| | | || _ || |_| || _ || |
| |_| || |_| || || |_| || _ |
| || || || || | | |
|_ _|| || || _ | | |_| |
| | | _ || ||_|| || |_| || |
|___| |__| |__||_| |_||_______||_______|

<---> [01] Y(ambo) P(ost)/(re) P(rocessor)
<---> [02] Core DB
<---> :: Electrons : 44.00000
<---> :: Temperature [ev]: 0.000000
<---> :: Lattice factors [a.u.]: 24.94439 25.51130 10.01776
<---> :: K points : 13
<---> :: Bands : 400
<---> :: Symmetries : 2
<---> :: RL vectors : 400283
<---> [03] K-point grid
<---> :: Q-points (IBZ): 13
<---> :: X K-points (IBZ): 13
<---> [04] CORE Variables Setup
<---> [04.01] Unit cells
<---> [04.02] Symmetries
<---> [04.03] RL shells
<---> [04.04] K-grid lattice
<---> [04.05] Energies [ev] & Occupations
<---> [05] Excitonic Properties
<---> :: Sorting energies
<---> [M 1.547 Gb] Alloc WF ( 1.532)
<01s> [FFT-EXCWF] Mesh size: 123 125 49
<01s> [WF-EXCWF loader] Wfs (re)loading | | [000%] --(E) --(X)
<16s> [WF-EXCWF loader] Wfs (re)loading |####################| [100%] 14s(E) 14s(X)
<16s> [M 1.547 Gb] Free wf_disk ( 0.149)
<16s> [05.01] Excitonic Wave Function
<16s> [05.01.01] Real-Space grid setup
<16s> :: Extended grid : 123 125 49
<16s> :: Hole position in the DL cell [cc]: 0.00 0.00 0.00
<16s> :: position in the FFT grid [cc]: 0.00 0.00 0.00
<16s> :: translated position [cc]: 0.00 0.00 0.00
<16s> :: [A]: 0.00 0.00 0.00
<16s> Processing 1 states
<16s> ExcWF@1 | | [000%] --(E) --(X)[n69:21992] *** Process received signal ***
[n69:21992] Signal: Segmentation fault (11)
[n69:21992] Signal code: Address not mapped (1)
[n69:21992] Failing at address: 0x7ffff434fe10
[n69:21992] [ 0] /lib64/libpthread.so.0 [0x376ae0de70]
[n69:21992] [ 1] ypp(__intel_ssse3_rep_memcpy+0x1b77) [0x6319c7]
[n69:21992] [ 2] ypp(wf_apply_symm_+0x10d) [0x48b49d]
[n69:21992] [ 3] ypp(excitons_driver_+0x35f5) [0x4377a5]
[n69:21992] [ 4] ypp(ypp_i_+0xc39) [0x426b59]
[n69:21992] [ 5] ypp(main+0xd34) [0x4231b4]
[n69:21992] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x376a21d8b4]
[n69:21992] [ 7] ypp [0x4223c9]
[n69:21992] *** End of error message ***
Segmentation fault
----------------------------------------------------------------------------------------------------------------------------------------------------------------
what is the main reason? thanks

[Daniele Varsano]

Dear Hbshu,
I do supsect you are using an old revision of the code:
please have a look to this post.
It looks the same problem and it was a bug we fixed some months ago. So try to update to the last revision of the code.

Best,
Daniele