MD tutorial / How to use DL_POLY４
Masahiro Yamamoto since 2007 !!This is the open (x-hidden-x x-Non-linked-x) linked site!!
Please contact to M. Y. (masahiro@konan-u.ac.jp) before download
if you are not told about this site directly
from MY .
Also Please don't link this site .
Thank you. updated 2020/02/21
あなたは，
番目の訪問者です． I can't understad why so many people can reach this site?
Tutorials
1. What's MD? →
MD_Tutorial_1.pdf (0.9MB)
2. DL_POLY setup →
MD_Tutorial_2.pdf (0.5 MB)
3. LJ system:Ar atoms :gas, liquid. solid, supercritical state →
MD_Tutorial_3new.pdf (5.8MB)
4. LiCl molten salt system →
MD_Tutorial_4.pdf (1.8 MB)
5. Liquid Water: SPC/E and TIP4P/Ew →
MD_Tutorial_5.pdf (1.7 MB)
6. DCE: OPLS all atom model and potential is checked by ab-initio cal. →
MD_Tutorial_6.pdf (1.6MB)
7. HT-SAM on Au(111): HT SAM on Au(111) potentials are made from scratch. →
MD_Tutorial_7.pdf (1.6MB)
MD Source code DL_POLY (You need registration to Prof. W. Smith CSE Department, CCLRC
Daresbury Laboratory, UK) Please visit here!!.
DL_POLY_Classics (DL POLY 2)
and DL_POLY_4 (parallel)
Animations (so
what's?) VMD (visual MD) is used here. HISTORY
file can be easily visualised. Please visit here.
1. Ar atoms: gas,
liquid, solid, super-critical state
2. LiCl molten salt
3. Water: SPC/E water (NVE) , SPC/E water (NPT) , TIP4PEw water(NVE), TIP4PEw water(NPT)
4. DCE all atom DCE (NVE) all atom DCE (NPT)
Input files for
DL_POLY
"What's I learned here: There is no free lunch to do a
theoretical calculation. I think you will understand what I mean
soon."
If the Fortran used is very strict, please be
careful that the format of the input! Check the tutorial by Daresbury
Lab. PDF here
Ume-chan and Yuko-san took one year to work the code for IBM-Parallel machine!!
I. LJ system:Ar atoms:gas, liquid. solid, supercritical state
CONTROL_Ar_gas(new),
CONTROL_Ar_liquid_solid(new)
CONTROL_Ar_scs(new)
CONFIG_gas CONFIG_liquid CONFIG_solid CONFIG_scs
FIELD_Ar_gas FIELD_Ar_solid_liquid FIELD_Ar_scs
DLPOLY_LJinput.f
fcclatticemake.f
velocity_make.f
run
II. LiCl molten salt system:
CONTROL
CONFIG FIELD DLPOLY_LiClinput.f
III. Liquid Water:
SPC/E: CONTROL_NVE
CONTROL_NPT CONFIG FIELD DLPOLY_Water_SPCE.f
TIP4P/Ew: CONTROL_NVE
CONTROL_NPT
CONFIG FIELD DLPOLY_Water_TIP4P.f
IV. DCE: all atom
CONTROL_NVE CONTROL_NPT CONFIG FIELD
DLPOLY_DCE.f CONFIG_1mol_0K_cos3_update DLPOLY_DCEinput_random_orientation.f(new) オイラー角の解説はここ
V. Solute in Organic Solvent :From HISTORY file of solvent MD run, incert some number of solutes in it.
histrory_READandWrite_DCE_LiCl.f HISTORY
histrory_READandWrite_DCE_LiPF6.f (random orientation of PF6, PF6basis.txt should be prepaered. HISTORY is the same file. PF6basis.txt
VI. EC and PC solvent GONFIG make with random orientation
DLPOLY_EC.f CONFIG_EC
DLPOLY_PC.f CONFIG_PC
If you finish all, you can now start to cal. your system. I will
make your account on the high-performance machine of which the CPUs are one of
the fastest in the world. Please ask me.
I find an EXERCISES site in DL-POLY HP. Please visit here!!.
Please remind that 90 % of the people who want to study
BASIC(program language) will drop out in the end.!
Force
Field Database
Ionic liquids forcefield by J.N. Canongia Lopes => click here
2013 Oct Ionic liquids forcefield by J.N. Canongia Lopes => click here
click here
Database given by tinker code (you can get almost all major force
fields)=> HP here
Fortran入門 by NAG HP here プログラミング言語FORTRANとUNIXの知識が必要です！
→ Fortran検定 by NAG HP
here 質問に解答して証明書をもらおう！
→→ OPEN MP入門(演習付き) by NAG HP here 並列計算言語
→→→ FORTRAN2003入門 by NAG HP here
→→→→ FORTRANtips by NAG HP here
京大人環富田博之先生のFORTRANプログラミング(htmlへのリンク有）および本「改訂版 『Fortran90/95プログラミング』 （冨田・齋藤： 培風館）。（2011年4月）」がおすすめ
個人的に好きなFortran90の本 PDF passwd有り
Python
AI等への適用で，最近はやはり"Python"でしょという皆さんにはこちらが超お薦め！
喜多一先生の無料テキストですが，京大の先生の本はさすがです！深---い！！
Kyoto University Research Information Repository: プログラミング演習 Python 2019（最新版 2020/02/13）
プログラミング演習 Python 2019
喜多先生のinterview記事
UNIX/LINUX入門（とらりもん by 筑波大学流域管理研究室） HP
Here とりあえず中級まで！
The DL_POLY Molecular Simulation Package HP here