STATE tutorialOnline resources• STATE wiki
http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/• STATE document@Read the Docs
https://state-doc.readthedocs.io/en/latest/index.html• STATE examples
https://github.com/ikuhamada/state-examples

Outline• Introduction– Overview of STATE• Compilation and configuration– Obtaining the code
– Compiling the code
– Preparing the job script• Tutorial– Running the code
– Analysis and post-processing of the results

What is STATE?
• Total energy code based on density functional theory– Plane-wave basis set– Pseudopotentials (normconserving & ultrasoft)– Iterative diagonalization (Davidson/RMM-DIIS)– Various exchange-correlation functionals• Semilocal functional (LDA/GGA)• vdW inclusive functional (DFT-D2/vdW-DF)• On-site Hubbard correction (DFT+U)• Written in Fortran90• Parallelized with MPI & openMP• Parallelized over bands/k-points/G-vectors/images

People• Developers– Yoshitada Morikawa (Osaka University)– Kouji Inagaki (Osaka University)– Yuji Hamamoto (Osaka University)– Ikutaro Hamada (Osaka University)• Contributors– Zhong Fang (CAS)– Takashi Ikeda (JAEA)– Osamu Sugino (University of Tokyo)– Minoru Otani (AIST)– Makoto Haraguchi (System Numeric)– Teruo Hirakawa (Osaka University)… and many moreWhat can STATE compute?
• Total energy• Hellmann-Feynman force– Geometry optimization– Reaction path search bynudged elastic band (NEB) method– Finite temperature molecular dynamics– Constraint molecular dynamics– Metadynamics– Vibrational mode analysis

What can STATE do?
• Effective screening medium (ESM) method– Accurate slab calculation– Charged slab calculation– Constant charge & constant potential calculation

What can STATE do?
• Electronic structure analysis– Density of states– Band structure– Charge density / wave function plot
– Bader charge analysis via the Bader program• STM simulation• XPS (core level shift) simulation

What can STATE do?
Organic metal interfaces
Alq3

Morikawa, et al., Phys. Rev. B. 69, 041403 (2004).

Yanagisawa, et al., Phys. Rev. B. 83, 235412 (2011).

Yoshida, et al., Nano Lett.. 13, 481 (2013).
Hamada et al., Phys. Rev. B 85, 121401(R) (2012).

What can STATE do?
Catalytic reactions

Bui, et al., Appl. Phys. Lett. 107, 201601 (2015).

Hirakawa, et al., J. Phys. Chem. B. 121, 164 (2017).

Muttaqien, et al., Chem. Comm. 53, 9222 (2017).

What can STATE do?
Electrochemical reactions

Otani, et al., J. Phys. Soc. Jpn. 77, 024802 (2008).
Hamada and Sugino HYOMEN KAGAKU 34, 638 (2013).

Herron, Morikawa, Mavrikakis, Proc. Natl. Acad. Sci. USA 113, E4937 (2016).

Recommended textbook

Electronic Structure
Basic Theory and Practical Methods(Cambridge University Press)
Richard M. MartinTutorialOutline
Carbon monoxide (CO) & ethylene (C2H4)

Silicon (Si)

Aluminum (Al) and nickel (Ni)

Chlorine atom on an Aluminum (100) surface [Cl/Al(100)]SetupLogin$ ssh –Y [your_userID]@cmd2.phys.sci.Osaka-u.ac.jp

Setup of STATE (for CMD workshop)
In the home directory, type:$ ~teac21/STATE/util/setup-state-cmd.sh$ source ~/.bashrc
Type:
$ ls
STATE/$ cd STATE$ ls
examples/ gncpp@ src/
$ cd examples$ ls
Al/ C2H4/ ClonAl100/ CO/ Ni/ README.md Si/ util/

Input/output files
Ground state (SCF or single-point) calculation
Pseudopotentials

Input file

Potential/charge

Output file

Wave function

DOS fileCO molecule

Input file (nfinp_scf)
In the STATE directory$ cd examples/COSTATE legacy input (nfinp_dav)

Input file (nfinp_scf)$ cat nfinp_scf← Wave function optimization← # of atomic species← # of atoms← Cutoff wave vector for the wave function (GMAX2=Ecutwf (Ry))← Cutoff wave vector for the augmented charge (GMAXP2=Ecutden (Ry))← Max # of SCF steps← Mixing parameter for SCF← Smearing parameter for insulators (small number)← Convergence threshold for the total energy (Hartree/atom)← Number of bands← Cell parameters
A, B, C, ALPHA, BETA, GAMMA← Atomic types (NTYP lines)(legacy format)← Atomic coordinates (NTYP lines)(legacy format)

Lattice parameters

A
Length of the first lattice vector aCOB
Length of the second lattice vector b
CLength of the third lattice vector ccα

ALPHAAngle between lattice vectors b and cβabγ

BETA
Angle between lattice vectors c and aGAMMAAngle between lattice vectors a and b

Input file (nfinp_scf)

Atomic types

Atomic number Atomic mass (a.m.u.)

Dummy

Initial magnetization

Dummy Dummy

Input file (nfinp_scf)

Atomic coordinates

CARTESIAN or CRYSTAL

Input file (nfinp_scf)

X, Y, Z (TAU_X, TAU_Y, TAU_Z)

Dummy(always 1)

MD type: 1 (relax), 0 (fix)Index for the atomic type

Checking the input file
$ chkinpf nfinp_scf
PROGRAM chkinpf VERSION 1.5.4
READING nfinp_1...DONE.
GENERATING CO.xsf...DONE.
*INFO: ESTIMATED NUMBER OF VALENCE ELECTRONS: 10*INFO: PRIM. CELL VOLUME: 0.960000E+02 BOHR**3 = 14.225715 ANGSTROM**3$ VESTA CO.xsf

Job script (qsub_cmd.sh)$ cat qsub_cmd.sh← # of cores to be used

← STATE executable← Pseudos.

$ qsub qsub_cmd.sh

STATE output$ less nfout_1

STATE output
When SCF converges, following information is printed

STATE output
and also …

STATE output
If NOT SCF converged …

• Change the mixing parameter and restart when SCF convergence is not achieved.
• Change time step and restart when structural optimization is not achieved.

Silicon in the diamond structureInput/output files
Ground state (SCF or single-point) calculation
Pseudopotentials

pot.Si_pbe1

Input file

Potential/charge

Output file

Wave function

DOS file

Name of the pseudopotential can be arbitrary with new input interface

Input file (nfinp_scf)← Space group number← K-point mesh
← K-point shift (1: OFF, 2: ON)← Atomic species← Atomic coordinates in the crystal coordinate

Job script (qsub_cmd.sh)$ qsub qsub_cmd.shAluminum in the fcc structureInput file (nfinp_scf)← Smearing function for metals

Ferromagnetic Ni in the fcc structureInput file (nfinp_scf)← Spin polarization allowed← Initial magnetization

Geometry optimization
SCF

Update geometry
Restart files

SCF converge?

No

Save wave functions & exit

NoForce converge?
Yes
Save wave functions & exit
No restart file generated if 1st SCF does not converge

Input/output files
Geometry optimization

C2H4 molecule

Structural optimization

Input file (nfinp_gdiis)← Geometry optimization (GDIIS)← Force threshold (Hartree/Bohr)Molecular dynamics
SCF

Update trajectory
Restart files

SCF converge?

NoNo# of MD steps > Max. step?

Yes
Save wave functions & exit

Save wave functions & exit

Input/output files
Molecular dynamics simulation

Input file (nfinp_nhc)← Finite temperature molecular dynamics← Temperature (K)Cl on Al(100) (optional)

Converting the input file format
Use the utility program “chkinpf” to convert the legacy input to the new input:$ chkinpf --convert nfinp_1
Type the following for the available options:$ chkinpf --help

Have fun with STATE!

Units used in STATE• Hartree atomic unit
– 1 Hartree (Eh) = 1 a.u.
– 1 Rydberg = 0.5 a.u.
– 1 Bohr radius (Bohr) = 1 a.u.
– 1 electron rest mass (me) = 1 a.u.
– 1 elementary charge (e) = 1 a.u.
– 1 Planck’s constant ( ) = 1 a.u.
– 1 proton mass 1836 a.u.