Reduce timing of NEGF for Al

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Reduce timing of NEGF for Al

Date: 2016/08/02 12:59
Name: Hiroya Nakata <hiroya.nakata.gt@kyocera.jp>: Dear all,

I have a question about NEGF.

My NEGF calculation took 100 times
longer than the standard SCF calculation
for pure Al:
The standard scf took 3 minutes, while
it took 6~8 hours for NEGF, assuming that
there is some mistake in my input file.
(Both of them use 40 core)

Could anyone give some advice regarding
my input file shown bellow, in order to reduce
computational timing?

Thank you very much for your helps in advance.

Best regards,
Hiroya

-------------------------------Input file for NEGF--------------------
#
# File Name
#

System.Name Alnegf
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (1-3)
memory.usage.fileout off # default=off, on|off

#
# Definition of Atomic Species
#

Species.Number 1
<Definition.of.Atomic.Species
Al Al7.0-s3p3d2 Al_CA13
Definition.of.Atomic.Species>

#DATA.PATH /opt/openmx3.8/DFT_DATA13
DATA.PATH /home1/share/openmx/3.7.6/intel/impi/DFT_DATA13
#
#
# Atoms
#
#NEGF.output_hks on
#NEGF.filename.hks Al.lead.hks
#
Atoms.Number 64
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates # Unit=Ang.
1 Al 0.0000000 0.0000000 0.0000000 1.5 1.5
2 Al 0.0000000 2.0247500 2.0247500 1.5 1.5
3 Al 2.0247500 0.0000000 2.0247500 1.5 1.5
4 Al 2.0247500 2.0247500 0.0000000 1.5 1.5
5 Al 4.0495000 -0.0000000 0.0000000 1.5 1.5
6 Al 4.0495000 2.0247500 2.0247500 1.5 1.5
7 Al 6.0742500 0.0000000 2.0247500 1.5 1.5
8 Al 6.0742500 2.0247500 0.0000000 1.5 1.5
9 Al 0.0000000 4.0495000 0.0000000 1.5 1.5
10 Al 0.0000000 6.0742500 2.0247500 1.5 1.5
11 Al 2.0247500 4.0495000 2.0247500 1.5 1.5
12 Al 2.0247500 6.0742500 0.0000000 1.5 1.5
13 Al 4.0495000 4.0495000 0.0000000 1.5 1.5
14 Al 4.0495000 6.0742500 2.0247500 1.5 1.5
15 Al 6.0742500 4.0495000 2.0247500 1.5 1.5
16 Al 6.0742500 6.0742500 0.0000000 1.5 1.5
17 Al 0.0000000 0.0000000 4.0495000 1.5 1.5
18 Al 0.0000000 2.0247500 6.0742500 1.5 1.5
19 Al 2.0247500 0.0000000 6.0742500 1.5 1.5
20 Al 2.0247500 2.0247500 4.0495000 1.5 1.5
21 Al 4.0495000 -0.0000000 4.0495000 1.5 1.5
22 Al 4.0495000 2.0247500 6.0742500 1.5 1.5
23 Al 6.0742500 0.0000000 6.0742500 1.5 1.5
24 Al 6.0742500 2.0247500 4.0495000 1.5 1.5
25 Al 0.0000000 4.0495000 4.0495000 1.5 1.5
26 Al 0.0000000 6.0742500 6.0742500 1.5 1.5
27 Al 2.0247500 4.0495000 6.0742500 1.5 1.5
28 Al 2.0247500 6.0742500 4.0495000 1.5 1.5
29 Al 4.0495000 4.0495000 4.0495000 1.5 1.5
30 Al 4.0495000 6.0742500 6.0742500 1.5 1.5
31 Al 6.0742500 4.0495000 6.0742500 1.5 1.5
32 Al 6.0742500 6.0742500 4.0495000 1.5 1.5
33 Al 0.0000000 0.0000000 8.0990000 1.5 1.5
34 Al 0.0000000 2.0247500 10.1237500 1.5 1.5
35 Al 2.0247500 0.0000000 10.1237500 1.5 1.5
36 Al 2.0247500 2.0247500 8.0990000 1.5 1.5
37 Al 4.0495000 -0.0000000 8.0990000 1.5 1.5
38 Al 4.0495000 2.0247500 10.1237500 1.5 1.5
39 Al 6.0742500 0.0000000 10.1237500 1.5 1.5
40 Al 6.0742500 2.0247500 8.0990000 1.5 1.5
41 Al 0.0000000 4.0495000 8.0990000 1.5 1.5
42 Al 0.0000000 6.0742500 10.1237500 1.5 1.5
43 Al 2.0247500 4.0495000 10.1237500 1.5 1.5
44 Al 2.0247500 6.0742500 8.0990000 1.5 1.5
45 Al 4.0495000 4.0495000 8.0990000 1.5 1.5
46 Al 4.0495000 6.0742500 10.1237500 1.5 1.5
47 Al 6.0742500 4.0495000 10.1237500 1.5 1.5
48 Al 6.0742500 6.0742500 8.0990000 1.5 1.5
49 Al 0.0000000 0.0000000 12.1485000 1.5 1.5
50 Al 0.0000000 2.0247500 14.1732500 1.5 1.5
51 Al 2.0247500 0.0000000 14.1732500 1.5 1.5
52 Al 2.0247500 2.0247500 12.1485000 1.5 1.5
53 Al 4.0495000 -0.0000000 12.1485000 1.5 1.5
54 Al 4.0495000 2.0247500 14.1732500 1.5 1.5
55 Al 6.0742500 0.0000000 14.1732500 1.5 1.5
56 Al 6.0742500 2.0247500 12.1485000 1.5 1.5
57 Al 0.0000000 4.0495000 12.1485000 1.5 1.5
58 Al 0.0000000 6.0742500 14.1732500 1.5 1.5
59 Al 2.0247500 4.0495000 14.1732500 1.5 1.5
60 Al 2.0247500 6.0742500 12.1485000 1.5 1.5
61 Al 4.0495000 4.0495000 12.1485000 1.5 1.5
62 Al 4.0495000 6.0742500 14.1732500 1.5 1.5
63 Al 6.0742500 4.0495000 14.1732500 1.5 1.5
64 Al 6.0742500 6.0742500 12.1485000 1.5 1.5
Atoms.SpeciesAndCoordinates>
#
#
LeftLeadAtoms.Number 64
<LeftLeadAtoms.SpeciesAndCoordinates
1 Al 0.0000000 0.0000000 -16.1980000 1.5 1.5
2 Al 0.0000000 2.0247500 -14.1732500 1.5 1.5
3 Al 2.0247500 0.0000000 -14.1732500 1.5 1.5
4 Al 2.0247500 2.0247500 -16.1980000 1.5 1.5
5 Al 4.0495000 -0.0000000 -16.1980000 1.5 1.5
6 Al 4.0495000 2.0247500 -14.1732500 1.5 1.5
7 Al 6.0742500 0.0000000 -14.1732500 1.5 1.5
8 Al 6.0742500 2.0247500 -16.1980000 1.5 1.5
9 Al 0.0000000 4.0495000 -16.1980000 1.5 1.5
10 Al 0.0000000 6.0742500 -14.1732500 1.5 1.5
11 Al 2.0247500 4.0495000 -14.1732500 1.5 1.5
12 Al 2.0247500 6.0742500 -16.1980000 1.5 1.5
13 Al 4.0495000 4.0495000 -16.1980000 1.5 1.5
14 Al 4.0495000 6.0742500 -14.1732500 1.5 1.5
15 Al 6.0742500 4.0495000 -14.1732500 1.5 1.5
16 Al 6.0742500 6.0742500 -16.1980000 1.5 1.5
17 Al 0.0000000 0.0000000 -12.1485000 1.5 1.5
18 Al 0.0000000 2.0247500 -10.1237500 1.5 1.5
19 Al 2.0247500 0.0000000 -10.1237500 1.5 1.5
20 Al 2.0247500 2.0247500 -12.1485000 1.5 1.5
21 Al 4.0495000 -0.0000000 -12.1485000 1.5 1.5
22 Al 4.0495000 2.0247500 -10.1237500 1.5 1.5
23 Al 6.0742500 0.0000000 -10.1237500 1.5 1.5
24 Al 6.0742500 2.0247500 -12.1485000 1.5 1.5
25 Al 0.0000000 4.0495000 -12.1485000 1.5 1.5
26 Al 0.0000000 6.0742500 -10.1237500 1.5 1.5
27 Al 2.0247500 4.0495000 -10.1237500 1.5 1.5
28 Al 2.0247500 6.0742500 -12.1485000 1.5 1.5
29 Al 4.0495000 4.0495000 -12.1485000 1.5 1.5
30 Al 4.0495000 6.0742500 -10.1237500 1.5 1.5
31 Al 6.0742500 4.0495000 -10.1237500 1.5 1.5
32 Al 6.0742500 6.0742500 -12.1485000 1.5 1.5
33 Al 0.0000000 0.0000000 -8.0990000 1.5 1.5
34 Al 0.0000000 2.0247500 -6.0742500 1.5 1.5
35 Al 2.0247500 0.0000000 -6.0742500 1.5 1.5
36 Al 2.0247500 2.0247500 -8.0990000 1.5 1.5
37 Al 4.0495000 -0.0000000 -8.0990000 1.5 1.5
38 Al 4.0495000 2.0247500 -6.0742500 1.5 1.5
39 Al 6.0742500 0.0000000 -6.0742500 1.5 1.5
40 Al 6.0742500 2.0247500 -8.0990000 1.5 1.5
41 Al 0.0000000 4.0495000 -8.0990000 1.5 1.5
42 Al 0.0000000 6.0742500 -6.0742500 1.5 1.5
43 Al 2.0247500 4.0495000 -6.0742500 1.5 1.5
44 Al 2.0247500 6.0742500 -8.0990000 1.5 1.5
45 Al 4.0495000 4.0495000 -8.0990000 1.5 1.5
46 Al 4.0495000 6.0742500 -6.0742500 1.5 1.5
47 Al 6.0742500 4.0495000 -6.0742500 1.5 1.5
48 Al 6.0742500 6.0742500 -8.0990000 1.5 1.5
49 Al 0.0000000 0.0000000 -4.0495000 1.5 1.5
50 Al 0.0000000 2.0247500 -2.0247500 1.5 1.5
51 Al 2.0247500 0.0000000 -2.0247500 1.5 1.5
52 Al 2.0247500 2.0247500 -4.0495000 1.5 1.5
53 Al 4.0495000 -0.0000000 -4.0495000 1.5 1.5
54 Al 4.0495000 2.0247500 -2.0247500 1.5 1.5
55 Al 6.0742500 0.0000000 -2.0247500 1.5 1.5
56 Al 6.0742500 2.0247500 -4.0495000 1.5 1.5
57 Al 0.0000000 4.0495000 -4.0495000 1.5 1.5
58 Al 0.0000000 6.0742500 -2.0247500 1.5 1.5
59 Al 2.0247500 4.0495000 -2.0247500 1.5 1.5
60 Al 2.0247500 6.0742500 -4.0495000 1.5 1.5
61 Al 4.0495000 4.0495000 -4.0495000 1.5 1.5
62 Al 4.0495000 6.0742500 -2.0247500 1.5 1.5
63 Al 6.0742500 4.0495000 -2.0247500 1.5 1.5
64 Al 6.0742500 6.0742500 -4.0495000 1.5 1.5
LeftLeadAtoms.SpeciesAndCoordinates>

RightLeadAtoms.Number 64
<RightLeadAtoms.SpeciesAndCoordinates
1 Al 0.0000000 0.0000000 16.1980000 1.5 1.5
2 Al 0.0000000 2.0247500 18.2227500 1.5 1.5
3 Al 2.0247500 0.0000000 18.2227500 1.5 1.5
4 Al 2.0247500 2.0247500 16.1980000 1.5 1.5
5 Al 4.0495000 -0.0000000 16.1980000 1.5 1.5
6 Al 4.0495000 2.0247500 18.2227500 1.5 1.5
7 Al 6.0742500 0.0000000 18.2227500 1.5 1.5
8 Al 6.0742500 2.0247500 16.1980000 1.5 1.5
9 Al 0.0000000 4.0495000 16.1980000 1.5 1.5
10 Al 0.0000000 6.0742500 18.2227500 1.5 1.5
11 Al 2.0247500 4.0495000 18.2227500 1.5 1.5
12 Al 2.0247500 6.0742500 16.1980000 1.5 1.5
13 Al 4.0495000 4.0495000 16.1980000 1.5 1.5
14 Al 4.0495000 6.0742500 18.2227500 1.5 1.5
15 Al 6.0742500 4.0495000 18.2227500 1.5 1.5
16 Al 6.0742500 6.0742500 16.1980000 1.5 1.5
17 Al 0.0000000 0.0000000 20.2475000 1.5 1.5
18 Al 0.0000000 2.0247500 22.2722500 1.5 1.5
19 Al 2.0247500 0.0000000 22.2722500 1.5 1.5
20 Al 2.0247500 2.0247500 20.2475000 1.5 1.5
21 Al 4.0495000 -0.0000000 20.2475000 1.5 1.5
22 Al 4.0495000 2.0247500 22.2722500 1.5 1.5
23 Al 6.0742500 0.0000000 22.2722500 1.5 1.5
24 Al 6.0742500 2.0247500 20.2475000 1.5 1.5
25 Al 0.0000000 4.0495000 20.2475000 1.5 1.5
26 Al 0.0000000 6.0742500 22.2722500 1.5 1.5
27 Al 2.0247500 4.0495000 22.2722500 1.5 1.5
28 Al 2.0247500 6.0742500 20.2475000 1.5 1.5
29 Al 4.0495000 4.0495000 20.2475000 1.5 1.5
30 Al 4.0495000 6.0742500 22.2722500 1.5 1.5
31 Al 6.0742500 4.0495000 22.2722500 1.5 1.5
32 Al 6.0742500 6.0742500 20.2475000 1.5 1.5
33 Al 0.0000000 0.0000000 24.2970000 1.5 1.5
34 Al 0.0000000 2.0247500 26.3217500 1.5 1.5
35 Al 2.0247500 0.0000000 26.3217500 1.5 1.5
36 Al 2.0247500 2.0247500 24.2970000 1.5 1.5
37 Al 4.0495000 -0.0000000 24.2970000 1.5 1.5
38 Al 4.0495000 2.0247500 26.3217500 1.5 1.5
39 Al 6.0742500 0.0000000 26.3217500 1.5 1.5
40 Al 6.0742500 2.0247500 24.2970000 1.5 1.5
41 Al 0.0000000 4.0495000 24.2970000 1.5 1.5
42 Al 0.0000000 6.0742500 26.3217500 1.5 1.5
43 Al 2.0247500 4.0495000 26.3217500 1.5 1.5
44 Al 2.0247500 6.0742500 24.2970000 1.5 1.5
45 Al 4.0495000 4.0495000 24.2970000 1.5 1.5
46 Al 4.0495000 6.0742500 26.3217500 1.5 1.5
47 Al 6.0742500 4.0495000 26.3217500 1.5 1.5
48 Al 6.0742500 6.0742500 24.2970000 1.5 1.5
49 Al 0.0000000 0.0000000 28.3465000 1.5 1.5
50 Al 0.0000000 2.0247500 30.3712500 1.5 1.5
51 Al 2.0247500 0.0000000 30.3712500 1.5 1.5
52 Al 2.0247500 2.0247500 28.3465000 1.5 1.5
53 Al 4.0495000 -0.0000000 28.3465000 1.5 1.5
54 Al 4.0495000 2.0247500 30.3712500 1.5 1.5
55 Al 6.0742500 0.0000000 30.3712500 1.5 1.5
56 Al 6.0742500 2.0247500 28.3465000 1.5 1.5
57 Al 0.0000000 4.0495000 28.3465000 1.5 1.5
58 Al 0.0000000 6.0742500 30.3712500 1.5 1.5
59 Al 2.0247500 4.0495000 30.3712500 1.5 1.5
60 Al 2.0247500 6.0742500 28.3465000 1.5 1.5
61 Al 4.0495000 4.0495000 28.3465000 1.5 1.5
62 Al 4.0495000 6.0742500 30.3712500 1.5 1.5
63 Al 6.0742500 4.0495000 30.3712500 1.5 1.5
64 Al 6.0742500 6.0742500 28.3465000 1.5 1.5
RightLeadAtoms.SpeciesAndCoordinates>

#Atoms.UnitVectors.Unit Ang # Ang|AU
#<Atoms.UnitVectors # unit=Ang.
# 0.000 0.0000 16.1980
# 8.0990 0.0000 0.000
# 0.000 8.0990 0.000
#Atoms.UnitVectors>
#
NEGF.filename.hks.l Al.lead.hks
NEGF.filename.hks.r Al.lead.hks

NEGF.Num.Poles 100 # defalut=150
NEGF.scf.Kgrid 1 1 # defalut=1 1

NEGF.bias.voltage 1.0 # default=0.0 (eV)
NEGF.bias.neq.im.energy 0.01 # default=0.01 (eV)
NEGF.bias.neq.energy.step 0.02 # default=0.02 (eV)

#
#
# SCF or Electronic System
#
#
#
#
#
#

scf.XcType LDA # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization Off # On|Off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver NEGF # Recursion|Cluster|Band|Krylov
scf.Kgrid 1 1 4 # means 4x4x4
scf.Mixing.Type Rmm-Diis # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.05 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 5 # default=5
scf.Mixing.StartPulay 6 # default=6
scf.criterion 1.0e-07 # default=1.0e-6 (Hartree)

#
#
Dos.fileout on # on|off, default=off
#NEGF.Dos.energyrange -15.0 25.0 5.0e-3 #default=-10.0 10.0 5
#NEGF.Dos.energy.div 200 # default=200
#NEGF.Dos.Kgrid 1 1 # default=1 1

#
# MD or Geometry Optimization
#

MD.Type nomd # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.maxIter 1 # default=1
MD.TimeStep 0.5 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)

Page: [1]

Re: Reduce timing of NEGF for Al ( No.1 )

Date: 2016/08/02 17:15
Name: Artem Pulkin

Hi,

Yes, NEGF method is slower for 2 basic reasons:

1. Unlike in conventional DFT, in NEGF energy is an additional external parameter. During NEGF SC cycle you integrate over it.

2. The boundary conditions in NEGF are not periodic (they are fixed in one of the dimensions). Thus, obtaining Kohn-Sham potential takes more time. (Much more time considering the fact that the 'length' of your device has to be saturated). Moreover I am not sure whether this part is parallel.

From my personal experience, 8 hours is good enough for this number of atoms.

Artem

Page: [1]