PCoMS OpenMX Hands-on Seminar2020

overview & application form

What is OpenMX? OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The efficient implementation of DFT used in OpenMX enables us to investigate electronic, magnetic, and geometrical structures of a wide variety of materials such as biological molecules, carbon-based materials, magnetic materials, and nanoscale conductors. Even ab initio electronic structure calculations for systems consisting of more than 10000 atoms are possible with the O(N) method implemented in OpenMX if several thousands cores on a parallel computer are available. [cited from "User's manual of OpenMX Ver. 3.9" URL: http://www.openmx-square.org/]
Please participate in our seminar and try using OpenMX.

OpenMX(Open source package for Material eXplorer)は密度汎関数理論(DFT)、ノルム保存型擬ポテンシャルおよび擬原子基底関数に基づき、 原子レベルから物質の第一原理シミュレーションを実行するためのソフトウェア・パッケージです。 OpenMXにおいて実現されたDFTの効率的な実装により、炭素系材料、生体分子、磁性体およびナノスケール電気伝導体など幅広い物質の 幾何構造、電子構造、また磁気構造などを第一原理的に計算することが可能です。 数百コアを有する並列コンピュータを使用することにより、千個の原子で構成される系を通常の対角化手法を用いて扱うことができます。 さらに数千コアを有する並列コンピュータを使用すれば、一万個以上の原子から構成される系の第一原理による電子状態計算さえも、 OpenMXに実装されているO(N)法を用いて実行可能です。[「OpenMX Ver. 3.8 ユーザーマニュアル」より抜粋]

Date / 日程: 9:30 - 17:00, February 14(Fri), 2020

Venue / 会場: Lounge, 1st floor of 2nd Building,
Institute for Materials Research, Katahira Campus, Tohoku Univ.(2-1-1 Katahira, Aoba-ku, Sendai 980-8577)
Access map and campus map are here.
東北大学 片平キャンパス 金属材料研究所2号館 1階ラウンジ(宮城県仙台市青葉区片平2-1-1) 
Lecturer / 講師: Taisuke Ozaki(ISSP, Univ. of Tokyo)
Mitsuaki Kawamura (ISSP, Univ. of Tokyo)

Capacity / 定員: 13 participants who will be allowed to accesss a cluster machine. Besides 13 participants mentioned above, participants can attend without being allocated to have an account on the cluster machine.
If there are more than 13 applications, we will give priority to the PCoMS members.  
registration fee /
Financial support for travel expenses is available for
1. the members of PCoMS IPD program
2. doctoral course students, postdocs, and fixed-term assistant professor level researchers within ten years of their acquisition of the doctoral degree, who are member of Tohoku University, the University Tokyo, Osaka University and the Institute for Molecular Science.
For details please check the following remarks.

How to apply and
the deadline /

Please apply using following application form by February 7th (Fri) 16:00.
If you wish to get the financial support for travel expense, please apply by January. 31(Fri).

Overview / 概要: The hands-on workshop will provide a good opportunity to learn practical aspects of density functional theories (DFT) calculations in a concise way to students and researchers who are interested in DFT calculations by OpenMX. The series of lectures in the hands-on workshop will start from an introductory lecture on fundamentals of density functional theories (DFT), and followed by lectures concerning practical implementations of OpenMX and its advanced extensions. Each of lectures is accompanied with a tutorial session so that participants can experience actual calculations based on the lectures.

program /
9:30-10:40  Introduction of DFT and OpenMX
10:40-11:10  Hands-on lecture
11:10-12:00  Login to computer and perform test calculations 
12:00-13:00  Lunch break
13:00-13:30   Geometry optimization, NEB calculations, and molecular dynamics
13:30-14:10  Practical session (take a break properly)
14:10-14:40  Calculations of X-ray photoemission spectra
14:40-15:20  Practical session (take a break properly)
15:20-15:50  Electronic transport calculations by NEGF
15:50-16:30  Practical session (take a break properly)
16:30-17:00  Discussion session

Notes /
Notes to participants in the tutorial sessions
You should bring your laptop machine with X-terminal supporting ssh. You will be provided an account for a PC cluster installed in the ISSP so that you can login the machine via ssh and run OpenMX. The installation of OpenMX on the PC cluster will be done by the ISSP. We assume that you are familiar with linux and an editor such as vi and emacs. We will not have any course about how to use linux in the tutorial sessions. If you are not familiar with those computer literacy, we stongly recommend you to learn those issues as a homework before the participation of the hands-on workshop. As for the file transfer between your laptop and the PC cluster, we recommend software WinSCP for windows users. Also, we recommend OpenMX Viewer, VESTA and XCrySDen for visualization. The latter two software should be installed on your laptop machine before the participation. In addition, it is highly desirable gnuplot to be available on your laptop machine to quickly visualize data.
If you are asigned as a participant who will be allowed to accesss a cluster machine, please send us ( mkawamura@issp.u-tokyo.ac.jp ) your public key for ssh.

Lecture materials
The lecture materials will be available on the website. Please download them, and print out them by yourself before your participation if you need. Also, we provide you the English manual of OpenMX Ver. 3.9 at the venue.

financial support /

Those who wish to get the support are requested to join “PCoMS - Innovative Professional Development (IPD) Program (category: General or Fellow)”.
Please find requirements for completing IPD program (Fellow, General) & list of elective courses at
For the application, please visit
https://pcoms-office.imr.tohoku.ac.jp/ (for fellow / general)
If you are a member of IPD program, please indicate in the notes of application form that you want financial support for the travel expense.

Contact address /
Professional development Consortium for Computational Materials Scientists (PCoMS)
PCoMS office
(pcoms=imr.tohoku.ac.jp : Please replace = with @.)
東北大学金属材料研究所 計算物質科学人材育成コンソーシアム(PCoMS)事務局
メール: pcoms=imr.tohoku.ac.jp (=を@に変更してください。)

Cohost /
Professional development Consortium for Computational Materials Scientists(PCoMS)

ISSP, The University of Tokyo
東京大学 物性研究所

CCMS, The University of Tokyo
東京大学 物性研究所 計算物質科学研究センター

Cooperation /
協賛 :
Center for Computational Materials Science, Institute for Materials Research, Tohoku University
東北大学 金属材料研究所 計算材料学センター

Post-K Exploratory Challenge Challenge of Basic Science
- Exploring Extremes through Multi-Physics and Multi-Scale Simulations
ポスト「京」萌芽的課題 基礎科学の挑戦-複合・マルチスケール問題を通した極限の探求

Post-K Priority Issue 7
Creation of new functional Devices and high-performance Materials to Support next-generation Industries
ポスト「京」重点課題(7) 次世代の産業を支える新機能デバイス・高性能材料の創成

Post-K Priority Issue 5
Development of new fundamental technologies for high-efficiency energy creation, conversion/storage and use
ポスト「京」重点課題(5) エネルギーの高効率な創出、変換・貯蔵,利用の新規基盤技術の開発

"Materials research by Information Integration" Initiative

Application form (申込フォーム)

氏名/name:   性/family name    名/first name
department, lab :
email address:
email address confirm:
分類(身分・所属) /classification: 【PCoMS関係者 / PCoMS members】

【PCoMS以外 / Other】
専門分野/research field: (複数選択可/Multiple choices allowed)

研究手法/research methods: (複数選択可--Multiple choices allowed)

研究分野/research field 2: (複数選択可--Multiple choices allowed)

cluster machine access:
Yes, I want. No, I do'nt want.
If there are more than 13 applications, we will give priority to the PCoMS members.
備考/Notes: PCoMS事務局へのメッセージなどがございましたら、御記載ください。
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