Input variables
We here summarize namelists that appear in this Tutorial. A thorough list of the namelist variables may be found in the downloaded file in 'SALMON/manual/input_variables.md'.
Contents
&units
Mandatory: none
&units unit_system='A_eV_fs' /
This namelist specifies the unit system to be used in the input file. Options are 'A_eV_fs' for Angstrom, eV, and fs, and 'a.u.' or 'au' for atomic units. If you do not specify it, atomic unit will be used as default.
For isolated systems (specified by iperiodic = 0
in &system
), the unit of 1/eV is used for the output files of DOS and PDOS if unit_system = 'A_eV_fs'
is specified, while atomic unit is used if not. For other output files, the Angstrom/eV/fs units are used irrespective of the namelist value.
For periodic systems (specified by iperiodic =3
in &system
), the unit system specified by this namelist variable is used for most output files. See the first few lines of output files to confirm the unit system adopted in the file.
&calculation
Mandatory: calc_mode
&calculation calc_mode = 'GS' /
The value of the calc_mode
should be one of 'GS'
, 'RT'
, and 'GSRT'
. For isolated systems (specified by iperiodic = 3
in &system`), the ground state (`'GS'`) and the real time (`'RT'`) calculations should be done separately and sequentially. For periodic systems (specified by `iperiodic = 3` in
&system), both ground state and real time calculations should be carried out as a single task (
calc_mode = 'GS_RT'`).
For Maxwell + TDDFT multiscale calculation, add the following namelist.
use_ms_maxwell = 'y'
&control
Mandatory: none
&control sysname = 'C2H2' /
'C2H2' defined by sysname = 'C2H2'
will be used in the filenames of output files. If you do not specify it, the file name will start with 'default'.
&functional
&functional xc ='PZ' /
xc ='PZ'
indicates that (adiabatic) local density approximation is adopted (PerdewZunger: Phys. Rev. B23, 5048 (1981)). This is the default choice.
For isolated systems (specified by iperiodic = 0
in &system
), only the default choice of 'PZ' is available at present.
For periodic systems (specified by iperiodic = 3
in &system
), the following functionals may be available in addition to 'PZ':
xc = 'PZM'
PerdewZunger LDA with modification to improve sooth connection between high density form and low density one. :J. P. Perdew and Alex Zunger, Phys. Rev. B 23, 5048 (1981).
xc = 'TBmBJ' cval = 1.0
TranBlaha metaGGA exchange with PerdewWang correlation. :Fabien Tran and Peter Blaha, Phys. Rev. Lett. 102, 226401 (2009). John P. Perdew and Yue Wang, Phys. Rev. B 45, 13244 (1992). This potential is known to provide a reasonable description for the bandage of various insulators. For this choice, the additional mixing parameter 'cval' may be specified. If cval is set to a minus value, the mixingparameter will be computed following the formula in the original paper [Phys. Rev. Lett. 102, 226401 (2009)]. The default value for this parameter is 1.0.
Since version 1.1.0, exchangecorrelation functionals in Libxc library (http://www.tddft.org/programs/libxc/) have been usable in SALMON. At present, usable functionals are limited to LDA and GGA. For periodic systems, metaGGA functionals are usable as well. To specify the exchangecorrelation potentials of Libxc library, there are two ways. If the exchange and correlation potentials are given separately, you need to specify both alibx
and alibc
separately. If the exchange and correlation potentials are given as a combined set, you need to specify alibxc
. We show below an example:
&functional alibx = 'LDA_X' alibc = 'LDA_C_PZ' /
Available sets of the functionals are listed at the website http://www.tddft.org/programs/libxc/functionals/ .
Note that, the hybrid functionals (hybrid gga/mgga) are not supported in the current (version 1.1.0) of SALMON.
&system
Mandatory: iperiodic, al, nstate, nelem, natom
For an isolated molecule (Tutorial1, 2, 3):
&system iperiodic = 0 al = 16d0, 16d0, 16d0 nstate = 5 nelem = 2 natom = 4 nelec = 10 /
iperiodic = 0
indicates that the isolated boundary condition will be used in the calculation. al = 16d0, 16d0, 16d0
specifies the lengths of three sides of the rectangular parallelepiped where the grid points are prepared. nstate = 8
indicates the number of KohnSham orbitals to be solved. nelec = 10
indicate the number of valence electrons in the system. Since the present code assumes that the system is spin saturated, nstate
should be equal to or larger than nelec/2
. nelem = 2
and natom = 4
indicate the number of elements and the number of atoms in the system, respectively.
For a periodic system (Tutorial4, 5):
&system iperiodic = 3 al = 10.26d0,10.26d0,10.26d0 nstate = 32 nelec = 32 nelem = 1 natom = 8 /
iperiodic = 3
indicates that three dimensional periodic boundary condition (bulk crystal) is assumed. al = 10.26d0, 10.26d0, 10.26d0
specifies the lattice constans of the unit cell. nstate = 32
indicates the number of KohnSham orbitals to be solved. nelec = 32
indicate the number of valence electrons in the system. nelem = 1
and natom = 8
indicate the number of elements and the number of atoms in the system, respectively.
For Maxwell  TDDFT multi scale calculation (Tutorial6):
&system iperiodic = 3 al = 10.26d0,10.26d0,10.26d0 isym = 8 crystal_structure = 'diamond' nstate = 32 nelec = 32 nelem = 1 natom = 8 /
The difference from the above case is the variables, isym = 8
and crystal_structure = 'diamond'
, which indicates that the spatial symmetry of the unit cell is used in the calculation. Although the use of the symmetry substantially reduces the computational cost, it should be used very carefully. At present, the spatial symmetry has been implemented only for the case of the diamond structure.
&pseudo
Mandatory: pseudo_file, izatom
For C2H2 molecule:
&pseudo izatom(1)=6 izatom(2)=1 pseudo_file(1)='C_rps.dat' pseudo_file(2)='H_rps.dat' lmax_ps(1)=1 lmax_ps(2)=0 lloc_ps(1)=1 lloc_ps(2)=0 /
Parameters related to atomic species and pseudopotentials. izatom(1) = 6
specifies the atomic number of the element #1. pseudo_file(1) = 'C_rps.dat'
indicates the filename of the pseudopotential of element #1. lmax_ps(1) = 1
and lloc_ps(1) = 1
specify the maximum angular momentum of the pseudopotential projector and the angular momentum of the pseudopotential that will be treated as local, respectively.
For crystalline Si:
&pseudo izatom(1)=14 pseudo_file(1) = './Si_rps.dat' lloc_ps(1)=2 /
izatom(1) = 14
indicates the atomic number of the element #1. pseudo_file(1) = 'Si_rps.dat'
indicates the pseudopotential filename of element #1. lloc_ps(1) = 2
indicate the angular momentum of the pseudopotential that will be treated as local.
&atomic_coor
Mandatory: atomic_coor or atomic_red_coor (they may be provided as a separate file)
For C2H2 molecule:
&atomic_coor 'C' 0.000000 0.000000 0.599672 1 'H' 0.000000 0.000000 1.662257 2 'C' 0.000000 0.000000 0.599672 1 'H' 0.000000 0.000000 1.662257 2 /
Cartesian coordinates of atoms. The first column indicates the element. Next three columns specify Cartesian coordinates of the atoms. The number in the last column labels the element.
&atomic_red_coor
Mandatory: atomic_coor or atomic_red_coor (they may be provided as a separate file)
For a crystalline silicon:
&atomic_red_coor 'Si' .0 .0 .0 1 'Si' .25 .25 .25 1 'Si' .5 .0 .5 1 'Si' .0 .5 .5 1 'Si' .5 .5 .0 1 'Si' .75 .25 .75 1 'Si' .25 .75 .75 1 'Si' .75 .75 .25 1 /
Cartesian coordinates of atoms are specified in a reduced coordinate system. First column indicates the element, next three columns specify reduced Cartesian coordinates of the atoms, and the last column labels the element.
&rgrid
Mandatory: dl or num_rgrid
This namelist provides grid spacing of Cartesian coordinate system. dl(3)
specify the grid spacing in three Cartesian coordinates. This is adopted for C2H2 calculation (Tutorial1).
&rgrid dl = 0.25d0, 0.25d0, 0.25d0 /
num_rgrid(3)
specify the number of grid points in each Cartesian direction. This is adopted for crystalline Is calculation (Tutorial4, 5, 6).
&rgrid num_rgrid = 12,12,12 /
&kgrid
Mandatory: none
This namelist provides grid spacing of kspace for periodic systems.
&kgrid num_kgrid = 4,4,4 /
&scf
Mandatory: nscf
This namelists specify parameters related to the selfconsistent field calculation.
&scf ncg = 4 nscf = 1000 convergence = 'norm_rho_dng' threshold_norm_rho = 1.d15 /
ncg = 4
is the number of conjugategradient iterations in solving the KohnSham equation. Usually this value should be 4 or 5. nscf = 1000
is the number of scf iterations. For isolated systems specified by &system/iperiodic = 0
, the scf loop in the ground state calculation ends before the number of the scf iterations reaches nscf
, if a convergence criterion is satisfied. There are several options to examine the convergence. If the value of norm_rho_dng
is specified, the convergence is examined by the squared difference of the electron density,
&hartree
Mandatory: none
&hartree meo = 3 num_pole_xyz = 2,2,2 /
meo
specifies the order of multipole expansion of electron density that is used to prepare boundary condition for the Hartree potential.

meo=1
: Monopole expansion (spherical boundary condition). 
meo=2
: Multipole expansions around each atom. 
meo=3
: Multipole expansion around the center of mass of electrons in cubits that are defined bynum_pole_xyz
.
num_pole_xyz(3)
defines the division of space when meo = 3
is specified.
A default for meo
is 3
, and defaults for num_pole_xyz
are (0,0,0)
. When default is set for num_pole_xyz
, the division of space is carried out using a prescribed method.
&tgrid
Mandatory: dt, Nt
&tgrid dt=1.25d3 nt=5000 /
dt=1.25d3
specifies the time step of the time evolution calculation. nt=5000
specifies the number of time steps in the calculation.
&propagation
This namelist specifies the numerical method for time evolution calculations of electron orbitals.
&propagation propagator='etrs' /
propagator = 'etrs'
indicates the use of enforced timereversal symmetry propagator. M.A.L. Marques, A. Castro, G.F. Bertsch, and A. Rubio, Comput. Phys. Commun., 151 60 (2003).
&propagation propagator='middlepoint' /
propagation='middlepoint'
indicates that Hamiltonian at midpoint of twotimes is used.
The default is middlepoint.
&emfield
This namelist specifies the pulse shape of an electric filed applied to the system in time evolution calculations. We explain below separating two cases, #Linear response calculations and #Pulsed electric field calculations.
Linear response calculations
A weak impulsive field is applied at t=0. For this case, ae_shape1 = 'impulse'
should be described.
Mandatory: ae_shape1
&emfield ae_shape1 = 'impulse' epdir_re1 = 0.d0,0.d0,1.d0 /
epdir_rel(3)
specify a unit vector that indicates the direction of the impulse.
For a periodic system specified by iperiodic = 3
, one may add trans_longi
. It has the value, 'tr'
(transverse) or 'lo'
(longitudinal), that specifies the treatment of the polarization in the time evolution calculation. The default is 'tr'
.
&emfield trans_longi = 'tr' ae_shape1 = 'impulse' epdir_re1 = 0.,0.,1. /
The magnitude of the impulse of the pulse may be explicitly specified by, for example, e_impulse = 1d2
. The default is '1d2' in atomic unit.
Pulsed electric field calculations
A Pulsed electric field of finite time duration is applied. For this case, as_shape1
should be specified. It indicates the shape of the envelope of the pulse. The options include 'Acos2' and 'Ecos2' (See below for other options).
Mandatory: ae_shape1, epdir_re1, {rlaser_int1 or amplitude1}, omega1, pulse_tw1, phi_cep1
&emfield ae_shape1 = 'Ecos2' epdir_re1 = 0.d0,0.d0,1.d0 rlaser_int_wcm2_1 = 1.d8 omega1=9.28d0 pulse_tw1=6.d0 phi_cep1=0.75d0 /
ae_shape1 = 'Ecos2'
specifies the envelope of the pulsed electric field, 'Ecos2' for the cos^2 envelope for the electric field. If 'Acos2' is specified, this gives cos^2 envelope for the vector potential. Note that 'phi_cep1' must be 0.75 (or 0.25) if one employs 'Ecos2' pulse shape, since otherwise the time integral of the electric field does not vanish. There is no such restriction for the 'Acos2' pulse shape.
epdir_re1 = 0.d0,0.d0,1.d0
specifies the real part of the unit polarization vector of the pulsed electric field. If only the real part is specified, it describes a linearly polarized pulse. Using both real ('epdir_re1') and imaginary ('epdir_im1') parts of the polarization vector, circularly (and general ellipsoidary) polarized pulses may be described.
laser_int_wcm2_1 = 1.d8
specifies the maximum intensity of the applied electric field in unit of W/cm^2. It is also possible to specify the maximum intensity of the pulse by amplitude1
.
omega1=9.26d0
specifies the average photon energy (frequency multiplied with hbar).
pulse_tw1=6.d0
specifies the pulse duration. Note that it is not the FWHM but a full duration of the cos^2 envelope.
phi_cep1=0.75d0
specifies the carrier envelope phase of the pulse. As noted above, 'phi_cep1' must be 0.75 (or 0.25) if one employs 'Ecos2' pulse shape, since otherwise the time integral of the electric field does not vanish. There is no such restriction for the 'Acos2' pulse shape.
It is possible to use two pulses simultaneously to simulate pumpprobe experiments, adding information for two pulses. To specify the second pulse, change from 1 to 2 in the namelist variables, like ae_shape2
. The time delay between two pulses is specified by the variable 't1_t2'.
For a periodic system specified by iperiodic = 3
, one may add trans_longi
. It has the value, 'tr'
(transverse) or 'lo'
(longitudinal), that specifies the treatment of the polarization in the time evolution calculation. The default is 'tr'
. For a periodic system, it is also specify 'Acos3', 'Acos4', 'Acos6', 'Acos8' for ae_shape1
.
&analysis
Mandatory: none
The following namelists specify whether the output files are created or not after the calculation. In the ground state calculation of isolated systems (Tutorial1):
&analysis out_psi = 'y' out_dns = 'y' out_dos = 'y' out_pdos = 'y' out_elf = 'y' /
In the time evolution calculation of isolated systems (Tutorial3):
&analysis out_dns_rt = 'y' out_elf_rt = 'y' out_estatic_rt = 'y' /
In the following namelists, variables related to timefrequency Fourier analysis are specified.
&analysis nenergy=1000 de=0.001 /
nenergy=1000
specifies the number of energy steps, and de=0.001
specifies the energy spacing in the timefrequency Fourier transformation.
&multiscale
This namelist specifies information necessary for Maxwell  TDDFT multiscale calculations.
&multiscale fdtddim = '1D' twod_shape = 'periodic' nx_m = 4 ny_m = 1 hX_m = 250d0 nxvacl_m = 2000 nxvacr_m = 256 /
fdtddim
specifies the spatial dimension of the macro system. fdtddim='1D'
indicates that onedimensional equation is solved for the macroscopic vector potential.
nx_m = 4
specifies the number of the macroscopic grid points in for xdirection in the spatial region where the material exists.
hx_m = 250d0
specifies the grid spacing of the macroscopic grid in xdirection.
nxvacl_m = 2000
and nxvacr_m = 256
indicate the number of grid points in the vacuum region, nxvacl_m
for the left and nxvacr_m
for the right from the surface of the material.
¶llel
When you execute a job with MPI parallelization, you are not required to specify any parameters that describe the assignment of the parallelization; the assignment is carried out automatically. You may also specify the parameters explicitly as below.
Mandatory: none
¶llel nproc_ob = 1 nproc_domain = 1,1,1 nproc_domain_s = 1,1,1 /

nproc_ob
specifies the number of MPI parallelization to divide the electron orbitals. The default value is 0 (automatic parallelization). 
nproc_domain(3)
specifies the number of MPI parallelization to divide the spatial grids of the electron orbitals in three Cartesian directions. The default values are (0/0/0) (automatic parallelization). 
nproc_domain_s(3)'
specifies the number of MPI parallelization to divide the spatial grids related to the electron density in three Cartesian directions. The default values are (0/0/0) (automatic parallelization).
The following conditions must be satisfied.
 The total number of processors must be equal to both
nproc_ob * nproc_domain(1) * nproc_domain(2) * nproc_domain(3)
and alsonproc_domain_s(1) * nproc_domain_s(2) * nproc_domain_s(3)
. 
nproc_domain_s(1)
is a multiple ofnproc_domain(1)
, and the same relations to the second and third components.