SALMON TUTORIAL, TSUKUBA, 2018

Introduction
About SALMON software package
and Explanation of Tutorial Menu

Masashi Noda
Center for Computer Science, University of Tsukuba
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/

1What is SALMON?
Scalable Ab-initio Light-Matter simulator
for Optics and Nanoscience• Real-time electron dynamics• Massive parallelization• Non-linear optical response• Couple with Maxwell equation

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 20182Overview of SALMON
K. Yabana and G. F. Bertsch, Phys. Rev. B 54, 4484 (1996)
ARTEDGCEED• solid/surface• laser damage• attosecond• nanostructure (multiscale)• cluster/surface/interface• optical near field• bias voltage• nanostructure (microscale)

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 2018

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TDDFT codes• TDDFT codes (frequency domain)
VASP, Quantum Espresso, Abinit, Gaussian, Q-Chem, GAMESS and so on …
• Real-time TDDFT codes Octopus
code widely used to describe electron dynamics
 FPSIDutilization of plane-wave basis, calculation for molecular dynamics
 Qboxplane-wave first-principles code, a large-scale calculation
 SIESTA, Elk FP-LAPW
utilization of numerical atomic orbitals
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20184

License• Web page:• http://salmon-tddft.jp• License: Apache 2.0• Mailing list: salmon-user@salmon-tddft.jp (contact address for inquiry)
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20185

Developers• Isabella Floss (TU Wien, Austria)• Yuta Hirokawa (University of Tsukuba, Japan)• Kenji Iida (Institute for Molecular Science, Japan)• Kazuya Ishimura (Institute for Molecular Science, Japan)• Kyung-Min Lee (Max Planck Institute for the Structure and Dynamics of Matter, Germany)• Katsuyuki Nobusada (Institute for Molecular Science, Japan)• Masashi Noda (University of Tsukuba, Japan)• Tomohito Otobe (National Institutes for Quantum and Radiological Science and Technology, Japan)• Shunsuke Sato (Max Planck Institute for the Structure and Dynamics of Matter, Germany)• Yasushi Shinohara (University of Tokyo, Japan)• Takashi Takeuchi (University of TsukubaInstitute for Molecular Science, Japan)• Xiao-Min Tong (University of Tsukuba, Japan)• Mitsuharu Uemoto (University of Tsukuba, Japan)• Kazuhiro Yabana (University of Tsukuba, Japan)• Atsushi Yamada (University of Tsukuba, Japan)• Shunsuke Yamada (University of Tsukuba, Japan)• Maiku Yamaguchi (University of Tokyo, Japan)
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 2018

(Alphabetic order)
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Pseudopotential and Functional• pseudopotential files
 Yabana-Bertsch format
 .pspnc (ABINIT format:

https://www.abinit.org/sites/default/files/PrevAtomicData/psp-links/psp-links/lda_tm)
 .cpi and .fhi (fhi98PP format:
https://www.abinit.org/sites/default/files/PrevAtomicData/psp-links/psp-links/lda_fhi)• Exchange-Correlation functions
Isolatedsystems

Periodicsystems

LDA-PZ (Perdew-Zunger LDA)

LSDA-PZ (Perdew-Zunger LSDA)

PAM (Perdew-Zunger LDA with modification)

TBmBJ (Tran-Blaha meta-GGA exchange withPerdew-Wang correlation)

LibXC without kinetic terms



Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 2018

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Parallelization• isolated systems
Kohn-Sham orbital: 𝜓𝑛 (𝒓)• periodic systems
Bloch orbital: 𝑢𝑛𝒌 (𝒓) MPI: orbital and domain

 MPI: k points

𝜓1∼10
𝜓11∼20𝜓21∼30𝜓31∼40𝜓1∼10
𝜓11∼20𝜓21∼30𝜓31∼40𝑢1∼10,𝟏∼𝟒 𝑢1∼10,𝟓∼𝟖𝑢11∼20,𝟏∼𝟒 𝑢11∼20,𝟓∼𝟖𝑢21∼30,𝟏∼𝟒 𝑢21∼30,𝟓∼𝟖𝑢31∼40,𝟏∼𝟒 𝑢31∼40,𝟓∼𝟖

domain division (2×2×2)

 OpenMP: domain OpenMP: orbital and k points

This parallelization is done automatically.
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20188

Performance (1)Ag54@Si454

Ag146@Si345

The K computer (RIKEN)Time steps: 1000

Diameter: 2.5nm

SystemCPU performance

Ag54@Si454

12.1% (1,944 processes)

Ag146@Si345

9.2% (4,000 processes)

Calculations for product runs end in 1.4 hours.
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 2018

9Performance (2)Au14144nm

The K computer (RIKEN)
Number ofprocesses

CPUperformance

7,800

11.0%

15,6009.3%

Calculations for product runs
end in 7 hours with 15,600
processes.

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201810

Performance (3)Laser Excitation Silicon Nanosphere

Computation~250 nm

SiE(t)EM Energy

Excitation Energy• World-class many-core supercomputer“Oakforest-PACS” (OFP)•••~ 24,000 [Node Hours] for Computation

Processer:• Intel Xeon Phi 7250
(68 cores 1.4GHz base clock)Number of Nodes:• 8208 nodes (use up to 8192)
Theoretical Peak Performance• 25 PFLOPS

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201811

Program: Exercise-1
14:15-16:15, November 12
Exercise-1. Installation of SALMON• Log-in to Super-computer• Build and Install• Submit Job

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 201812

Program: Exercise-2 & Exercise-3
16:30-17:30, November 12
Exercise-2. How to use SALMON – Isolated Systems• Input file format• Calculations of the ground state, polarizability
and photoabsorption of C2H2 molecule• Calculation of electron dynamics in C2H2
molecule under a pulsed electric field
14:00-15:00, November 13
Exercise-3. How to use SALMON – Periodic Systems• Calculation of the ground state• Calculations of dielectric function of crystalline
silicon• Calculations of electron dynamics in crystalline
silicon under a pulsed electric field
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 201813

Program: Exercise-4
15:15-17:15, November 13
Exercise-4. How to use SALMON – Advanced Options

4-1 Visualization

4-3 Optimization andNonadiabatic Molecular Dynamics

4-2 Multi-scale simulation

4-4 FDTD simulation

Incident light

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 2018Scatter

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Information
Download the PDF filesof the tutorial slide http://salmon-tddft.jp/download/tutorial2018-pdf.zip

https://salmon-tddft.jp
Download of a source
and a manual

Web manual

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201815

Information (continued)
Download ofa source file

Web manual

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 201816