AIMD Tutorial 2018 08 31 Goal Part 1

AIMD Tutorial 2018 -08 -31

Goal • Part 1 : (A) to (B) • Try to calculate yourself • Check the start & final structure, energy (A 0) Initial structure ac-plane ab-plane OPT 1. 8 Å (B) (A) Move Na AIMD At 0. 20 ps 3. 6 Å (D) OPT Move Na (X) OPT

Initial structure • VNL Builder Add From database ‘graphene’ 불러오기 • Builders surface(cleave) redefine & making supercell (8 x 4) • Export configuration . cif 형식으로 저장 VEST에서 불러들인 후 Export VASP 파일 ‘POSCAR’로 저장 • Supercell (8 x 4) + Na-ion

INCAR (For AIMD) • NSW = 5000 ! # of steps • IBRION = 0 ! how the ions are updated and moved; Verlet algorithm for AIMD ! Others for relaxations into a local energy minimum ! SMASS allows additional control • ISIF = 2 ! Fixed cell (volume) parameter & ionic relaxation • SMASS = 0 ! canonical ensemble is simulated using the algorithm of Nosé • POTIM = 0. 5 [fs] ! Time-step • TEBEG = 300 [K] ! Room Temp. ; control the temperature during an ab-initio mulecular dynamics ! No initial velocities on the POSCAR file the velocities set randomly (Maxwell-Boltzmann distribution) -------------------------------------------------------------------------- • # PREC = High ! Precision; set ENCUT if no values is given for ENCUT • ENCUT = 600 [e. V] ! Cut-off energy for plane wave basis set in e. V • ISPIN = 2 ! spin polarized calculations • NELM = 999 ! maximum number of electronic SC (self-consistency) steps • IDIPOL = 3 ! dipole moment

KPOINT Start cal. • POSCAR – constraint of atoms • $ Selective dynamics POTCAR • T: move / F: fix • Xshell • $ qsub [script file] POSCAR 1: Comment line 2: Lattice constant 3 -5: lattice vector 6 -7: atomic species and number of atoms 8: Selective dynamics (optional) 9: Cartesian of in direct (fractional) Coordinates of atoms Switch on or not ‘Selective dynamics’ (F=fix, T=move)

(B) (A) After cal. After • Energy graph – ORIGIN • grep "T= " OSZICAR | awk '{ print $1 " "$3 “ "$5 “ "$9 “ "$11 }‘ > Energy. txt • N is the number of electronic steps • E the total free energy (including the kinetic energy of the ions and the energy) • d. E the change in the free energy • F total free energy • E 0 is the energy for sigma 0 OUTCAR • contributions to electronic energy at each electronic iteration • convergence information: each electronic step • Movie – VMD • Eigenvalues: each ionic step • vasprun. xml • DOS + charge density: each ionic step • $ pbc box ! Draw a line of periodic boundary • total energy and electronic contributions: each ionic step • $ pbc wrap • Stress: each ionic step • $ pbc unwrap • basis vectors: each ionic step • Forces: each ionic step

Download-1 • For initial guess … • /pyelem/VASP/05_Na+graphene/01_opt • WAVECAR • CHGCAR

Download-2 Result files and command for extracting energies • pyelem/VASP/05_Na+graphene/02_aimd • stdout. out • OUTCAR • CONTCAR • XDATCAR • OSZICAR • vasprun. xml • By command: $ cp [filename] [directory] • Energy graph • $ grep "T= " OSZICAR | awk '{ print $1 " "$3 " "$5 " "$9 " "$11 }' > OSZICAR. txt