X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

xTAPP tutorial

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Computational Physics– First-Principles Electronic Structure Calculation –

S. TsuneyukiDepartment of Physics, the University of Tokyo

Jan. 13, 2016

The tutorial is based on the material prepared by Dr. Kanako Yoshizawa

X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCATutorial Cu（１）

• Texthttp://white.phys.s.u-tokyo.ac.jp/~yoshiz-k/example-cu.pdf (Japanese)http://white.phys.s.u-tokyo.ac.jp/~yoshiz-k/example-cu_en.pdf (English)

• Make directory ($HOME/xtapp/cu)$ mkdir cuChange directory ($HOME/xtapp/cu)$ cd cu

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X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA Tutorial Cu（２）# main data

&tappinput

lattice_factor = 6.90772,

lattice_list = 0.5, 0.5, 0.0,

0.5, 0.0, 0.5,

0.0, 0.5, 0.5,

cutoff_wave_function = 7.0,

number_element = 1,

number_atom = 1,

number_band = 12,

store_wfn = 1,

initial_lpt = 2,

scf_number_iter_1st = 40,

scf_number_iter = 40,

xc_type = ‘PBE’,

control_uptime = 7200.0 3

# symmetry data&symmetrysymmetry_format = ‘reciprocal’,number_sym_op = 24/

1 0 0 0 1 0 0 0 1 0 0 00 1 0 0 0 1 1 0 0 0 0 00 0 1 1 0 0 0 1 0 0 0 01 0 0 0 0 1 0 1 0 0 0 00 0 1 0 1 0 1 0 0 0 0 00 1 0 1 0 0 0 0 1 0 0 0

-1 -1 -1 0 1 0 0 0 1 0 0 0-1 -1 -1 0 0 1 0 1 0 0 0 0-1 -1 -1 1 0 0 0 0 1 0 0 0-1 -1 -1 0 0 1 1 0 0 0 0 0-1 -1 -1 1 0 0 0 1 0 0 0 0-1 -1 -1 0 1 0 1 0 0 0 0 00 1 0 -1 -1 -1 0 0 1 0 0 00 0 1 -1 -1 -1 0 1 0 0 0 01 0 0 -1 -1 -1 0 0 1 0 0 00 0 1 -1 -1 -1 1 0 0 0 0 01 0 0 -1 -1 -1 0 1 0 0 0 00 1 0 -1 -1 -1 1 0 0 0 0 00 1 0 0 0 1 -1 -1 -1 0 0 00 0 1 0 1 0 -1 -1 -1 0 0 01 0 0 0 0 1 -1 -1 -1 0 0 00 0 1 1 0 0 -1 -1 -1 0 0 01 0 0 0 1 0 -1 -1 -1 0 0 00 1 0 1 0 0 -1 -1 -1 0 0 0

X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

Tutorial Cu（３）

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# atom data

11 29

1 0.0 0.0 0.0

# k-points data

&smpl_kpt

dos_mode = 'COS',

dos_mesh = 32, 32, 32,

bz_mesh = 32,

bz_number_tile = 1

/

17 17 17

2 2 2

# struct_opt data

&struct_opt

number_cycle = 0

/

# str_opt_constr data

1

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X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

Tutorial Cu（４）• Calculation of charge density

Run inipot$ XTAPP_PS_DIR=/usr/share/xtapp/pseudo-potential/PBE/PS$ export FORT10=./cu.cg$ export FORT34=$XTAPP_PS_DIR/ps-Cu $ export FORT28=$XTAPP_PS_DIR/ps-Cu.ichr (Please set initial_lpt = 2) $ inipot > inipot.log$ less cgmrpt.log (check log file)

Run cgmrpt$ export FORT10=./cu.cg FORT11=./cu.lpt FORT25=./cu.rho$ export FORT96=./cu.wfn FORT99=./cu.str( $ export OMP_NUM_THREADS=8 [ If your machine has 8 threads ] )$ cgmrpt > cgmrpt.log$ less cgmrpt.log (check log file)

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X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCATutorial Cu（５）

• Calculation of band structure$ cp cu.cg cu.pef

Rewrite cu.pefAdd the following parameters at “# main data” in Cu.pefinitial_lpt = 1store_wfn = 1 → store_wfn = 0

Add “# trace band data” parameters in Cu.pef# trace band data&trace_banddistrib_mode = ‘none’,

output_wave_function = 1,number_trace_block = 7

/G X K G L K W X

1.0 1.0 0.750 0.0 0.5 0.750 0.75 0.50.0 0.5 0.375 0.0 0.5 0.375 0.25 0.00.0 0.5 0.375 0.0 0.5 0.375 0.50 0.5

10 5 10 10 10 5 56

X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

Tutorial Cu（６）Run vbpef$ export FORT10=./cu.pef FORT50=./cu.band FORT58=./cu.wfk$ export FORT11=./cu.lpt( $ export OMP_NUM_THREADS=8 [ If your machine has 8 threads ] )

$ vbpef > vbpef.log$ less vbpef.log (check log file)

Plot the band structure$ vbpef2gp-lsda –fcu –e[EF] ./cu.band$ gnuplotgnuplot> load “cu.gp”gnuplot> quit

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X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

• View the band structureChoose the [file] menuSelect the [Load Band data…]Open cu.band

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Tutorial Cu（７）

X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

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Tutorial Cu（８）

X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

Tutorial Cu（９）• Calculation of density of states (DOS)

$ cp cu.pef cu.w2c

Rewrite cu.w2cAdd the following parameters at “# main data” in Cu.w2cinitial_wfn = 1initial_lpt = 1 → initial_lpt = 0

Add “# inspect wfn data” parameters in Cu.w2c# inspect wfn data&inspect_wfndistrib_mode = pdos,pdos_target_atom = 1

/

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X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

Tutorial Cu（１０）Run wfn2chg$ XTAPP_PWAV_DIR=/usr/share/xtapp/pseudo-potential/PBE/pwav$ export FORT10=./cu.w2c $ export FORT18=$XTAPP_PWAV_DIR/ps-Cu.pwav.d$ export FORT95=./cu.wfn$ export FORT55=./cu.bunpu.d( $ export OMP_NUM_THREADS=8 [ If your machine has 8 threads ] )$ wfn2chg > wfn2chg.log$ less wfn2chg.log (check log file)

Plot the projected DOS$ ltzpdos cu.bunpu.d 300 0.0 1.2 0.010$ gnuplotgnuplot> plot “cu.bunpu.d.pdos” u 1:2, “cu.bunpu.d.pdos” u 1:3gnuplot> quit

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X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

• View the DOSChoose the [file] menuSelect the [Load Dos data…]Open cu.bunpu.d.pdos

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Tutorial Cu（１１）

X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

• View the Fermi SurfaceConvert cu.wfn to cu.???.ee.dx$ wfn2ee cu ‘1 1 0’ ‘1 0 1’ ‘0 1 1’ ‘-16 -16 -16’ ‘32 32 32’The “wfn2ee” is a tool to plot the Fermi surface from the orbital energy in a wave function file. The tool can expand to plot the surface in the extended zone. In the above instance, you expand it in a cubic extended zone, divide the zone into 32 x 32 x 32, and set the center of the zone just on the Gamma point.

Create cu.???.ee.dx??? : band index

Choose the [file] menuSelect the [Load Field data…]Open the cu.6.ee.dx

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Tutorial Cu（１２）

X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

Choose the [Graphics] menuOpen a [Graphics settings] dialog box to to select the [Field]

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Input the Fermi energy [Hatree]See cu.str (fort.99)

Tutorial Cu（１３）

X TAPPeXtended Tokyo Ab-initio Program Package

TAPIOCA

Fermi Surface of Cu

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Tutorial Cu（１４）