Manual for the legacy STATE input

Warning

This page is under construction

The current STATE code can also read an input file in the legacy fixed format. Here is an example of a CO molecule in a small box with the Gamma-point sampling:

 0  0  0  0  0  0                      : dummy line (6 integers)
 5.50 20.00  2  2  2                   : GMAX, GMAXP, NTYP, NATM, NATM2
 1  0                                  : NUM_SPACE_GROUP TYPE
 6.00  4.00  4.00  90.00  90.00  90.00 : A, B, C, ALPHA, BETA, GAMMA
 1  1  1  1  1  1                      : KNX, KNY, KNZ, K-POINT SHIFT
 1  0                                  : NCORD, NINV
 0.0000  0.0000  0.0000  1  1  1       : CPS, IWEI, IMDTYP, ITYP
 2.2000  0.0000  0.0000  1  1  2       : CPS, IWEI, IMDTYP, ITYP
 6  0.1500  51577.50 3 1 0.d0          : IATOMN, ALFA, AMION, ILOC, IVAN, ZETA1
 8  0.1500  51577.50 3 1 0.d0          : IATOMN, ALFA, AMION, ILOC, IVAN, ZETA1
 0  0  0  0  0                         : ICOND, INIPOS, INIVEL, ININOSE, INIACC
 0  1                                  : IPRE, IPRI
 200  200   0    57200.00  0           : NMD1, NMD2, ITER_LAST, CPUMAX, IFSTOP
 3   1                                 : WAY_MIX, MIX_WHAT
 0    8  0.8                           : STARTING_MIXING, KMXMIX, MIX_ALPHA
 0.60  0.50  0.60  0.70  1.00          : DTIM1, DTIM2, DTIM3, DTIM4, DTIM_LAST
 30.00    2     1  0.10D-08 1.d-06     : DTIO, IMDALG, IEXPL, EDELTA
  0.0010  0.10D+02    0                : WIDTH, FORCCR, ISTRESS
ggapbe          1                      : XCTYPE, NSPIN
  1.00                                 : DESTM
102                                    : NBZTYP
   0   0   0                           : NKX,  NKY,  NKZ  (dummy)
   0   0   0                           : NKX2, NKY2, NKZ2 (dummy)
   8                                   : NEG (# of bands)
       1                               : NEXTST (1: G-space, 0: R-space)
       0                               : 0 (dummy, set to 0)
       2                               : IMSD (2: Davidson, 1: RMM)
       0                               : EVAL_EKO_DIFF
       0                               : NPDOSAO
       0    0.0                        : SM_dopping (dummy)

In the following, each line/block is described one by one.

Dummy line

Dummy 6 integers

0  0  0  0  0  0                      : dummy line (6 integers)

For historical reason this line remains and needs to be given in the input file. Note that this line is/was used by a utility program “repeat.f.”

Cuotff energies, number of atomic species, number of atoms

5.50 20.00  2  2  2                   : GMAX, GMAXP, NTYP, NATM, NATM2

  • GMAX: Maximum wave number corresponding to the kinetic energy cutoff (in Rydberg) for the wave functions. \(E_{\rm{cut}}^{\rm{wf}} = {\rm{GMAX}}^2\)

  • GMAXP: Maximum wave number corresponding to the kinetic energy cutoff (in Rydberg) for the augmenation charge. \(E_{\rm{cut}}^{\rm{dens}} = {\rm{GMAXP}}^2\)

  • NTYP: Number of atomic species.

  • NATM: Number of inequivalent atoms by the inversion symmetry in the unit cell.

  • NATM2: Number of total atoms in the unit cell.

In the current version, inversion symmetry is not taken into account and thus always NATM should equal to NATM2.

Symmetry and bravis lattice type

1  0                                  : NUM_SPACE_GROUP, TYPE

  • NUM_SPACE_GROUP: space group number

  • TYPE: Bravis lattice type

TYPE

Bravis lattice

0

simple

1

body-centered

2

face-centered

3

a-face-centered

4

b-face-centered

5

c-face-centered

6

rhombohedral

Definition of the primitive cell vectors:

  • TYPE=0

\[ \begin{align}\begin{aligned}{\mathbf a}_1 = \tilde{\mathbf{a}}_1\\{\mathbf a}_2 = \tilde{\mathbf{a}}_2\\{\mathbf a}_3 = \tilde{\mathbf{a}}_3\end{aligned}\end{align} \]

  • TYPE=1

\[ \begin{align}\begin{aligned}{\mathbf a}_1 = -\tilde{\mathbf{a}}_1 + \tilde{\mathbf{a}}_2 + \tilde{\mathbf{a}}_3\\{\mathbf a}_2 = +\tilde{\mathbf{a}}_1 - \tilde{\mathbf{a}}_2 + \tilde{\mathbf{a}}_3\\{\mathbf a}_3 = +\tilde{\mathbf{a}}_1 + \tilde{\mathbf{a}}_2 - \tilde{\mathbf{a}}_3\end{aligned}\end{align} \]

  • TYPE=2

\[ \begin{align}\begin{aligned}{\mathbf a}_1 = \tilde{\mathbf{a}}_2 + \tilde{\mathbf{a}}_3\\{\mathbf a}_2 = \tilde{\mathbf{a}}_1 + \tilde{\mathbf{a}}_3\\{\mathbf a}_3 = \tilde{\mathbf{a}}_1 - \tilde{\mathbf{a}}_2\end{aligned}\end{align} \]

  • TYPE=3

\[ \begin{align}\begin{aligned}{\mathbf a}_1 = \tilde{\mathbf{a}}_1\\{\mathbf a}_2 = \tilde{\mathbf{a}}_2\\{\mathbf a}_3 = \frac12 \left( \tilde{\mathbf{a}}_2 + \tilde{\mathbf{a}}_3 \right)\end{aligned}\end{align} \]

  • TYPE=4

\[ \begin{align}\begin{aligned}{\mathbf a}_1 = \tilde{\mathbf{a}}_1\\{\mathbf a}_2 = \tilde{\mathbf{a}}_2\\{\mathbf a}_3 = \frac12 \left( \tilde{\mathbf{a}}_1 + \tilde{\mathbf{a}}_3 \right)\end{aligned}\end{align} \]

  • TYPE=5

\[ \begin{align}\begin{aligned}{\mathbf a}_1 = \tilde{\mathbf{a}}_1\\{\mathbf a}_2 = \frac12 \left( \tilde{\mathbf{a}}_1 + \tilde{\mathbf{a}}_2 \right)\\{\mathbf a}_3 = \tilde{\mathbf{a}}_3\end{aligned}\end{align} \]

  • TYPE=6

\[ \begin{align}\begin{aligned}{\mathbf a}_1 = +\frac23 \tilde{\mathbf{a}}_1 + \frac13 \tilde{\mathbf{a}}_2 + \frac13 \tilde{\mathbf{a}}_3\\{\mathbf a}_2 = -\frac13 \tilde{\mathbf{a}}_1 + \frac13 \tilde{\mathbf{a}}_2 + \frac13 \tilde{\mathbf{a}}_3\\{\mathbf a}_3 = -\frac13 \tilde{\mathbf{a}}_1 - \frac23 \tilde{\mathbf{a}}_2 + \frac13 \tilde{\mathbf{a}}_3\end{aligned}\end{align} \]

where \(\tilde{\textbf{a}}_1\), \(\tilde{\textbf{a}}_2\), \(\tilde{\textbf{a}}_3\) are the lattice vectors of the conventional unit cell (see below).

Lattice vectors

6.00  4.00  4.00  90.00  90.00  90.00 : A, B, C, ALPHA, BETA, GAMMA

  • A, B, C: length of the first, second, and third lattice vectors of the conventional cell.

  • ALPHA, BETA, GAMMA: Angles between second and third, third and first, and first and second lattice vectors.

In this way, the first lattice vector of the primitive cell \(\tilde{\textbf{a}}_1\) is along the x-axis, the second lattice vector \(\tilde{\textbf{a}}_2\) is in the xy plane, and the third vector \(\tilde{\textbf{a}}_3\) is determined depending on the angle with \(\tilde{\mathbf{a}}_1\) and \(\tilde{\mathbf{a}}_2\). In this example, the lattice vectors are given in the Bohr radius as

\[ \begin{align}\begin{aligned}\tilde{{\mathbf a}}_1 = (6.0, 0.0, 0.0)\\\tilde{{\mathbf a}}_2 = (0.0, 4.0, 0.0)\\\tilde{{\mathbf a}}_3 = (0.0, 0.0, 4.0)\end{aligned}\end{align} \]

Alternatively, one can define the lattice vectors by using the keyword “Cartesian” followed by the lattice vectors in the Cartesian coordinate as:

Cartesian
 6.00  0.00  0.00
 0.00  4.00  0.00
 0.00  0.00  4.00

Note

Use TYPE=0 when the lattice vectors are given in the cartesian coordinate, if you are unsure about the definition of the lattice vectors other than the cubic cell.

K-point mesh

1  1  1  1  1  1                      : KNX, KNY, KNZ, K_POINT SHIFT

First 3 integers are used to define the k-point mesh. Remaining 3 integers are used to define the k-point shift [1 for nonshifted grid and 2 for shifted grid (Monkhorst-Pack grid)].

Note

For the hexagonal systems, it is recommended to use nonshifted k-point grid to avoid the symmetry breaking.

Unit of the atomic coordinate, inversion symmetry

1  0                                  : NCORD, NINV

  • NCORD

1

Cartesian coordinate (in Bohr radius)

0

reduced coordinate (coordinate in the unit of primitive lattice vectors)

2

coordinate in the unit of conventional lattice vectors

  • NINV

0

no inversion symmetry

1

inversion symmetry

_note:: NINV=0 is not maintained in the current version of STATE, but the number of atoms can be almost halved when NINV=1 is activated, if it is implemented.

Atomic positions and types

0.0000  0.0000  0.0000  1  1  1       : CPS, IWEI, IMDTYP, ITYP
2.2000  0.0000  0.0000  1  1  2       : CPS, IWEI, IMDTYP, ITYP

  • 1-3 columns: CPS (POS) Atomic coordinates.

  • 4th column: IWEI Number of equivalent atoms by the inversion symmetry (OBSOLETE)

  • 5th colum: IMDTYP Set 1 when the atom is allowed to move, otherwise set 0.

  • 6th column: ITYP Atomic type

(Pseudo) atoms

6  0.1500  51577.50 3 1 0.d0          : IATOMN, ALFA, AMION, ILOC, IVAN, ZETA1
8  0.1500  51577.50 3 1 0.d0          : IATOMN, ALFA, AMION, ILOC, IVAN, ZETA1

  • 1st column: IATOMN Atomic number (real)

  • 2nd column: ALFA Initial charge (dummy real number)

  • 3rd column: AMION Atomic mass in a.m.u.

  • 4th column: ILOC Angular momentum for the local potential (l_loc +1) (dummy integer number)

  • 5th column: IVAN Integer to specify if ultrasoft pseudopotential is used (1) or not (0) (dummy integer number)

  • 6th column: ZETA1 Initial magnetization

Restart options for the wave functions

0  0  0  0  0                         : ICOND, INIPOS, INIVEL, ININOSE, INIACC

  • ICOND: Restart option for the wave functions and option for the electronic structure analysis

0

Initialize the wave function. This is used to start an SCF calculation from scratch.

1

Restart SCF by using the existing wave function and charge density (potential). zaj.data and potential.data are necessary.

2

Fixed charge calculation. Wave functions are calculated from scractch. potentil.data is necessary.

3

Restart the fixed charge calculation.

4

Fixed charge calculation (same as ICOND=2).

9

Print the total charge density in real space.

11

Print the soft part of the charge density in real space.

10

Simple STM simulation.

12

DOS calculation.

13

Old ALDOS

14

Partial density of states (PDOS/AO_LDOS) calculation (DOS projected onto the atomic orbitals).

21

STM simulation with the wave functions reconstructed in the vacuum region

24

K-point resolved partial density of states (PDOS) calculation.

15

Print the wave functions in real space.

115

Print the wave functions in real space. Used for the band structure calculation (ICOND=22)

17

Crystal orbital overlap population (COOP) analysis

117

K-point resolved crystal orbital overlap population (COOP) analysis

22

Band structure calculation.

23

Restart the band structure calculation.

33

Atomic layer resolved density of states (ALDOS) calculation.

40

Generate wave functions and potential.data for GWST (version 5.3.8b)

41

Generate wave functions along the high symmetry points and potentials for GWST (version 5.3.8b)

  • INIPOS: Restart options for the atomic positions

0

Read the atomic positions from the input file.

1

Restart by reading the atomic positions from “restart.data.”

2

Restart by reading the atomic positions from “GEOMETRY” (restart.data is also required).

  • INIVEL: Restart options for the atomic positions

0

Initialize the velocity

1

Restart by reading the velocities from “restart.data.”

2

Restart by reading the velocities from “GEOMETRY” (restart.data is also required).

  • ININOS: Restart options for the Nose thermostat

0

Initialize the thermostat

1

Restart the thermostat

  • INIACC: Restart options for the accumulator

0

Initialize the accumulator

1

Restart the accumulator

  • Examples of restart

Restart only SCF (geometry from input)

1  0  0  0  0                         : ICOND,INIPOS,INIVEL,ININOS, INIACC

Restart the structural optimization

1  1  0  0  0                         : ICOND,INIPOS,INIVEL,ININOS, INIACC

Restart the structural optimization by referring the GEOMETRY file

1  2 0  0  0                         : ICOND,INIPOS,INIVEL,ININOS, INIACC

Restart the structural optimization, but refresh the wave functions

0  1  0  0  0                         : ICOND,INIPOS,INIVEL,ININOS, INIACC

Restart the molcular dynamics

1  1  1  0  0                         : ICOND,INIPOS,INIVEL,ININOS, INIACC

or

1  1  1  1  1                         : ICOND,INIPOS,INIVEL,ININOS, INIACC

Stress, print level

0  1                                  : IPRE, IPRI

  • IPRE: 1 for the stress calculation (not implemented)

  • IPRI: verbosity of the output. Use IPRI>1 for debugging.

Numbef of SCF, structural optimization/MD, CPU time

200  200   0    57200.00  0           : NMD1, NMD2, ITER_LAST, CPUMAX, IFSTOP

  • NMD1: Maximum number of SCF steps.

  • NMD2: Maximum number of molecular dynamics step. NMD2+1 is the actural number of steps.

  • ITER_LAST

  • CPUMAX: Maximu CPU time in second.

  • IFSTOP

Mixing scheme, object to be mixed

3   1                                 : WAY_MIX, MIX_WHAT

  • WAY_MIX

1

simple mixing

2

Broyden

3

Broyden2

4

DFP

5

Pulay

6

Blugel

  • MIX_WHAT

1

charge density

2

potential

Mixing parameter

0    8  0.8                           : STARTING_MIXING, KMXMIX, MIX_ALPHA

  • STARTING_MIXING: The step charge/potenial mixing starts

  • KBXMIX: number of previous charges/potentials to be used in the mixing.

  • MIX_ALPHA: mixing parameter.

Mixing parameters for RMM-DIIS

0.60  0.50  0.60  0.70  1.00          : DTIM1, DTIM2, DTIM3, DTIM4, DTIM_LAST

  • DTIM: Mixing parameter for RMM-DIIS. Only DTIM2 is used.

  • DTIM_LAST: Dummy.

Time step, MD algorithm, convergence threshold

30.00    2     1  0.10D-08 1.d-06     : DTIO,IMDALG,IEXPL,EDELTA

  • DTIO: Molecular dynamics time step in the atomic unit (1 a.u.=0.024188 fs, 41.3428 a.u.=1 fs)

  • IMDALG: Molecular dynamics algorithm.

1

Newtonian dynamics

2

Quenched molecular dynamics

3

Vibrational mode analysis¡(nfvibrate.data required)

4

GDIIS

5

TS search by GDIIS

6

Nudged elastic band method

7

Climbing image NEB method

0

Newtonian dynamics

-1

Finite temperature Newtonian dynamics¡

-2

Langevin MD

  • IEXPL: dummy integer (to be used for the wave function extrapolation)

  • EDELTA: Threshold (total energy per atom) for the electronic system. Use 1.d-9 - 1.d-11.

Smearing, force threshold, stress

0.0010  0.10D+02    0                : WIDTH, FORCCR, ISTRESS

  • WIDTH: Smearing width. Use negative value (>-10.0) for the Hermite-Gaussian smearing. Use a value < -10.0 for the tetrahedron method.

  • FORCCR: Force threshold for the structural optimization. Use a large value (1.D+2 - 1.D+3) for an SCF calculation.

  • ISTRESS: 1 for stress calculation (not yet implemented)

Exchange correlation and spin

ggapbe          1                      : XCTYPE, NSPIN

  • XCTYPE

ggapbe

Perdew, Burke, Ernzerhof GGA (1996)

ggapw91

Perdew-Wang GGA (1991)

ldapw91

Perdew-Wang L(S)DA (1991)

rpbe

revised PBE of Hammer et al.

revPBE

revised PBE of Zhang and Yang

wc

Wu-Cohen GGA

vdW-DF

vdW-DF of Dion et al’s (vdW-DF2)

vdW-DF2

vdW-DF of Lee et al’s

optB88-vdW

vdW-DF of Klimes et al’s

optPBE-vdW

vdW-DF of Klimes et al’s

optB86b-vdW

vdW-DF of Klimes et al’s

vdW-DF-C09

vdW-DF-C09 of Cooper

vdW-DF2-C09

vdW-DF2-C09 of Hamada and Otani

vdW-DF-cx

vdW-DF-cx of Berland and Hyldgaard

rev-vdW-DF2

vdW-DF of Hamada’s

  • NSPIN

1

For a spin unpolarized system

2

For a spin polarzed system

STM

1.00                                 : DESTM

  • DESTM: STM bias in volt.

Type of sampling of G-vectors for the tetrahedron method

102                                    : NBZTYP

  • NBZTYP: specify how to sampel G vectors in the tetrahedron method. NBZTYP=101 is recommended

Dummy line

3 dummy integers:

0   0   0                           : NKX,  NKY,  NKZ  (dummy)

Dummy line

3 dummy integers:

0   0   0                           : NKX2, NKY2, NKZ2 (dummy)

Number of bands

8                                   : NEG (# of bands)

  • NEG: The number of bands considered in the calculation. Always use number of bands, which is slightly larger than the half of the number of valence electrons.

nonlocal pseudopotential scheme

1                               : NEXTST (1: G-space, 0: R-space)

  • NEXTST

0

R-space (Do not use when the Davidson scheme is usd)

1

G-space

Dummy line

0                               : 0; random numbers, 1; matrix diagon

Diagonalization method

2                               : IMSD (2: Davidson, 1: RMM)

  • IMSD

1

RMM-DIIS

2

Davidson

Note

For a large scale calculation, RMM-DIIS and real space projection is recommended (NEXTST=0 & IMSD=1). In such a case, prepare the wave functions with the Davidson scheme (NEXTST=1 & IMSD=2) and restart with RMM-DIIS.

Evaluate the eigenvalue difference

0                               : EVAL_EKO_DIFF: .0 = no ,1 = yes

  • EVAL_EKO_DIFF: Evaluate the eigenvalue difference from the previous step (1 to activate this). Unused currently.

PDOS option

0                                                   : NPDOSAO

When NPDOSAO>0, the PDOS calculation is performed. NPDOSAO indicates the number of atomic orbitals onto which DOSs are calculated. See below (to be completed).

Empirical parameters for the f electrons (dummy)

0    0.0

Optional input parameters

Charge of the system

&CHARGE … &END

This block specifies the charge of the system

Syntax:

&CHARGE
 CHARGE [value]
&END

CHARGE: The charge of the system. Positive (negative) value indicates that the system has deficit (execess) electron(s).

Effective screening medium (ESM) method

&ESM … &END

This block specifies the parameters for the ESM calculation.

Syntax:

&ESM
 BOUNDARY_CONDITION [boundary_condition]
 Z1 [value]
 CHARGE [value]
 Z_WALL [value]
 BAR_HEIGHT [value]
 BAR_WIDTH [value]
 ELECTRIC_FIELD [value]
&END

BOUNDARY_CONDITION: Boundary condition. Available options are BARE (PE0/BC1), PE1 (BC2), and PE2(BC3) for open (vacuum/slab/vacuum), metal/slab/metal, and vacuum/slab/metal boundary conditions, respectively

Z1: Z position of the cell boundary

CHARGE: Charge of the system. Note that positive value means deficit charge, while negative, excess charge.

Z_WALL: Z position of an artifical wall potential for electron

BAR_HEIGHT: Barrier height for the artifical wall potential for electron

BAR_WIDTH: Width for the artifical wall potential for electron

ELECTRIC_FIELD: Electric field (in Ha/Bohr) applied to the system. Use with the boundary condition PE1 (BC2).

Density of states

&DOS … &END

This block is used to define the parameters needed to calculate DOS.

EMIN: Minimum energy in eV.

EMAX: Maximum energy in eV.

NDOSE: Energy mesh for the density of states calculation.

EWIDTH: Smearing width for the Gaussian broadening

K-points for the band structure calculation

&KPOINTS_BAND … &END

This block is used to define the parameters needed in the band structure calculation.

NKSEG: Number of k-point segment for the band (the number of symmetry points should be NKSEG+1)

KMESH: K-point mesh for each segment.

KPOINTS: High symmetry k-points in the unit of the basic reciprocal lattice vectors (NKSEG+1 k-points should be specified). If ‘KPOINTS CART’ or ‘KPOINTS CARTESIAN’ is specified, they should be given in the unit of the cartesian coordinate.

Wave function plot

&PLOT … &END

This block define the parameters needed in the wave function plot.

IK/IKPT: K-point index at which the real-space wave functions are generated.

IB: Band index at which the wave function is generated

IBS/IBAND_S: The first band index for the wave function plot.

IBE/IBAND_E: The last band index for the wave function plot (IBS-th to IBE-th wave functions at the IK k-point are generated).

FORMAT: Format of the wave function can be specified

  • STATE: STATE format (not yet implemented)

  • CUBE: Gaussian Cube format (default)

  • XSF: Xcryden Structure File

  • XSF_CHARGE/CHARGE_XSF: Charge densities corresponding to the specified wave functions in the Xcrysden Structure File format

PRTVLOC/PRT_VLOC/PRINT_VLOC: Local potential (sum of the local and Hartree potentials) in the Xcrysden Structure File format