%BLOCK BS_KPOINT_PATH
k1x k1y k1z
k2x k2y k2z
. . .
kNx kNy kNz
%ENDBLOCK BS_KPOINT_PATH

%block bs_kpoint_path
0.0 0.0 0.0
0.0 0.0 0.5
%endblock bs_kpoint_path

%BLOCK CLASSICAL_INFO
S1 R1x R1y R1z Ch1
S2 R2x R2y R2z Ch2
. . . . .
. . . . .
SN RNx RNy RNz ChN
%ENDBLOCK CLASSICAL_INFO

%block classical_info
O 19.7 21.8 22.6 -0.3
H 17.6 22.1 22.6 0.12
H 20.7 23.6 22.6 0.17
%endblock classical_info

• 0 - No dispersion correction
• 1 - Damping function from Elstner [J. Chem. Phys. 114(12), 5149-5155]
• 2 - First damping function from Wu and Yang (I) [J. Chem. Phys. 116(2), 515-524]
• 3 - Second damping function from Wu and Yang (II) [J. Chem. Phys. 116(2), 515\u2013524]

See Proceedings of the Royal Society A 465(2103), 669\u2013683 for more details.

%BLOCK ETRANS_SETUP
source_start source_stop
drain_start drain_stop
%ENDBLOCK ETRANS_SETUP

In this example, the leads are made up from the atoms [61,120] and [361,420]. Note that the code assumes that those leads respectively couple with the central region via the atoms [121,180] and [301,360]. Eventually, the retarded Green's function associated will be computed for the atoms [61,420] (i.e. all other atoms are considered as "buffer atoms").

%block etrans_setup
061 120
361 420
%endblock etrans_setup

%BLOCK HUBBARD
S1 L1 U1 Z1 a1 s1
S2 L2 U2 Z2 a2 s1
. . . . .
. . . . .
SN LN UN ZN aN sN
%ENDBLOCK HUBBARD

%block hubbard
O 1 0.0 4.5 0.0 0.0
Fe 2 3.0 9.5 0.0 0.0
%endblock hubbard

This is only relevant in implicit solvent calculations and in calculations with open boundary conditions (such as calculations with smeared ions).

K^(n+1) = C_{in}K^{n}_{in} + C_{out}K^{n}_{out}

 w : residual: sqrt[sum(K_{out} - K_{in})^2]
 x : [HKS,SKH] commutator
 y : [K,KSK] commutator
 z : delta energy: E(n+1)-E(n)

Two or more elements activated means that the two criteria have to be true at the same time to achieve convergence (i.e. they have to be lower than kernel_diis_thres).

 D : for Hamiltonian diagonalisation only
 L : for kernel-linear mixing only.
 P : for Pulay-DIIS (linear mixing is used to generate the history of kernels)

%BLOCK LATTICE_CART
a1x a1y a1z
a2x a2y a2z
a3x a3y a3z
%ENDBLOCK LATTICE_CART

%block lattice_cart
7.500000 0.000000 0.000000 ; hexagonal unit cell with
-3.750000 6.495191 0.000000 ; a = 7.5 a0
0.000000 0.000000 9.000000 ; c = 9.0 a0
%endblock lattice_cart
or
%block lattice_cart
ang
50.000000 0.000000 0.000000 ; large cubic cell
0.000000 50.000000 0.000000 ;
0.000000 0.000000 50.000000 ;
%endblock lattice_cart

• 0 : no mixing, rely on COREHAM_DENSKERN_GUESS to initialize the density kernel at each MD step;
• 1 : use the density kernel optimized at the previous step as initial guess for the current SCF process;
• 2 : linear mixing of the MIX_DENSKERN_NUM former density kernels (see PRB 45, 1538 (1992) for further description of the algorithm);
• 3 : apply Christoffel corrections to the density kernel optimized at the previous step in order to account for the update of the NGWFs mixing;
• 4 : project the density kernel optimized at the previous step onto the current set of NGWFs;
• 5 : apply correction to the density kernel optimized at the previous step in order to preserve the KS product;
• 6 : time reversible propagation of an auxiliary density kernel (algorithm based on J. Chem. Phys. 130, 214109);
• 7 : (under development) dissipative propagation of an auxiliary density kernel (algorithm based on J. Chem. Phys. 130, 214109)).

• 0 : no mixing, rely on SPECIES_ATOMIC_SET to initialize the NGWFs at each MD step;
• 1 : use the NGWFs optimized at the previous step as initial guess for the current SCF process;
• 2 : linear mixing of the MIX_NGWFS_NUM former sets of NGWFs (see PRB 45, 1538 (1992) for further description of the algorithm);
• 3 : same algorithm as in 2, but using a different set of coefficients for each atom as a function of its local environment (relies on MIX_LOCAL_LENGTH and MIX_LOCAL_SMEAR in order to define the localization radius);
• 4 : polynomial extrapolation of the MIX_NGWFS_NUM former sets of NGWFs in real space;
• 6 : time reversible propagation of a set of auxiliary NGWFs (algorithm based on J. Chem. Phys. 130, 214109);
• 7 : (under development) dissipative propagation of a set of auxiliary NGWFs (algorithm based on J. Chem. Phys. 130, 214109)).

%BLOCK PADDED_LATTICE_CART
a1x a1y a1z
a2x a2y a2z
a3x a3y a3z
%ENDBLOCK PADDED_LATTICE_CART

%block padded_lattice_cart
100.00000 0.00000 0.00000 ; cubic unit cell
0.00000 100.00000 0.00000 ; side length 100 bohr
0.00000 0.000000 100.00000 ;
%endblock padded_lattice_cart

%BLOCK POSITIONS_ABS
S1 R1x R1y R1z
S2 R2x R2y R2z
. . . .
. . . .
SN RNx RNy RNz
%ENDBLOCK POSITIONS_ABS

%block positions_abs
C 5.0 5.0 5.0 ; CO2 molecule
O 2.7 5.0 5.0 ; centred in a cubic simulation cell
O 7.3 5.0 5.0 ; with sides of 10 a0
%endblock positions_abs

or

 psinc_spacing 0.25 0.25 0.25 ang 

%BLOCK SPECIES
S1 X1 Z1 n1 R1
S2 X2 Z2 n2 R2
. . . . .
. . . . .
SN XN ZN nN RN
%ENDBLOCK SPECIES

%block species
C1 C 6 4 6.0 ; species C1 is carbon with 4 NGWFs of radius 6.0 a0
C2 C 6 4 7.0 ; species C2 is also carbon but has 7.0 a0 NGWF radii
H H 1 1 5.0 ; species H is hydrogen with 1 NGWF of radius 5.0 a0
%endblock species

%BLOCK SPECIES_ATOMIC_SET
S1 <Fireball filename 1> | AUTO | SOLVE
S2 <Fireball filename 2> | AUTO | SOLVE
. .. .
%ENDBLOCK SPECIES_ATOMIC_SET

automatically as required.

%block species_atomic_set
C1 C_01.fbl
H AUTO
%endblock species_atomic_set

%BLOCK SPECIES_COND
S1 X1 Z1 n1 R1
S2 X2 Z2 n2 R2
. . . . .
. . . . .
SN XN ZN nN RN
%ENDBLOCK SPECIES

%block species
C1 C 6 9 12.0 ; species C1 is carbon with 9 NGWFs of radius 12.0 a0
C2 C 6 9 12.0 ; species C2 is also carbon but has 12.0 a0 NGWF radii
H H 1 4 10.0 ; species H is hydrogen with 4 NGWFs of radius 10.0 a0
%endblock species

%BLOCK SPECIES_CONSTRAINTS
S1 NONE | FIXED | LINE | PLANE [C1x C1y C1z]
. . . . .
%ENDBLOCK SPECIES_CONSTRAINTS

%block species_constraints
C1 FIXED ; atoms of species C1 are fixed
C2 LINE 1.0 0.0 0.0 ; atoms of species C2 can only move parallel to thex-axis
H PLANE 0.0 0.0 1.0 ; atoms of species H can only move in thexy-plane
%endblock species_constraints

%BLOCK SPECIES_LDOS_GROUPS
S1 S2 S3
. . .
%ENDBLOCK SPECIES_LDOS_GROUPS

%block species_ldos_groups
C1 H1 ; atoms of species C1 and H1 are in first group
C2 H2 ; atoms of species C1 and H1 are in second group
%endblock species_ldos_groups

%BLOCK SPECIES_NGWF_PLOT
S1
S2
.
%ENDBLOCK SPECIES_NGWF_PLOT

%block species_ngwf_plot
C1
C2
H
%endblock species_ngwf_plot

%BLOCK SPECIES_POT
S1 <Pseudopotential filename 1>
S2 <Pseudopotential filename 2>
. ..
%ENDBLOCK SPECIES_POT

%block species_pot
C1 C_01.recpot
C2 C_00.recpot
H H_01.recpot
%endblock species_pot

%BLOCK THERMOSTAT
time_start time_stop thermo_type thermo_temp
option1 = value1 (optional)
option2 = value2 (optional)
%ENDBLOCK THERMOSTAT

• time_start (integer): the time step at which the thermostat is initialized;
• time_stop (integer): the time step at which the thermostat is closed;
• thermo_type (text): the kind of thermostat to be used, currently NONE, ANDERSEN, LANGEVIN, or NOSEHOOVER;
• thermo_temp (physical): the thermostat temperature in physical units.

Each thermostat may also be tuned using the options,

• tgrad (physical): incremental temperature, in physical units, to be added at each time step;
• group (integer): specifies the group of atoms subjected to the thermostat (this option requires groups of atoms to be defined in POSITION_ABS);
• freq (real): characteristic thermostat's frequency,
  • if ANDERSEN : defines the collision probability via P_collision = 1-exp(-freq),
  • if NOSEHOOVER : specifies the thermostat coupling frequency in units of 1/MD_DELTA_T);
• damp (real): Langevin damping parameter;
• mix (real): mixing coefficient for a "softer" ANDERSEN thermostat (i.e. partial incorporation of the old momentum into the new momentum drawn from the Boltzmann distribution);
• nchain (integer): number of thermostats in the Nose-Hoover chain;
• nstep (integer): number of steps used to integrate the Nose-Hoover chain dynamics at each MD step;
• update (logical): if tgrad .ne. zero, then force new initialization of the Nose-Hoover thermostats masses at every MD steps.

In this example, the system is quenched from 3000 K using an ANDERSEN thermostat and then equilibrated by means of a Nose-Hoover chain. Here the value of the asymmetric stretching mode in water (0.053213/fs) has been used as the coupling frequency.

%block thermostat 
0001 1350  ANDERSEN  3000 K 
   tgrad = -2 K 
1351 5000 NOSEHOOVER 300 K 
   nchain = 4
   nstep = 8 
   freq = 0.053213 
%endblock thermostat

• LDA - default local (spin) density approximation, currently CAPZ
• GGA - default generalized gradient approximation, currently RPBE
• CAPZ - Perdew-Zunger parameterization [Phys. Rev. B23, 5048 (1981)] of the Ceperley-Alder Monte Carlo data [Phys. Rev. Lett.45, 566 (1980)] and Gell-Mann-Brueckner expansion [Phys. Rev.106, 364 (1957)]
• PW92 - Perdew and Wang 1992 LDA [Phys. Rev. B45, 13244 (1992)]
• VWN - Vosko, Wilk and Nusair parameterization [Phys. Rev. B22, 3812 (1980)] of the LDA
• PW91 - Perdew and Wang GGA [Phys. Rev. B45, 13244 (1992)]
• PBE - Perdew, Burke and Ernzerhof GGA [Phys. Rev. Lett.77, 3865 (1996) and Erratum]
• REVPBE - revised PBE by Zhang and Yang [Phys. Rev. Lett.80, 890 (1998)]
• RPBE - revised PBE by Hammer, Hansen and Norskov [Phys. Rev. B59, 7413 (1999)]
• BLYP -Becke 88 + LYP (Lee, Yang, Parr) GGA [Phys. Rev. A38, 3098 (1988); Phys. Rev. B37, 785 (1988)]
• XLYP - Xu and Goddard GGA [PNAS 101, 2673 (2004)]