Difference between revisions of "Tutorial-v.1.0.0"

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	We here summarize namelists that appear in this Tutorial.		We here summarize namelists that appear in this Tutorial.
−
−	=== &units ===
−
−	Mandatory: none
−
−	&units
−	unit_system='A_eV_fs'
−	/
−
−	This namelist specifies the unit system to be used in the input file.
−	If you do not specify it, atomic unit will be used.
−
−	For isolated systems (specified by <code>iperiodic = 0</code> in <code>&system</code>), the unit of 1/eV is used for the output files of DOS and PDOS if <code>unit_system = 'A_eV_fs'</code> 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.
−
−	=== &calculation ===
−
−	Mandatory: calc_mode
−
−	&calculation
−	calc_mode = 'GS'
−	/
−
−	The value of the <code>calc_mode</code> should be one of <code>'GS'</code>, <code>'RT'</code>, and <code>'GS-RT'</code>.
−	Note that the ground state (<code>'GS'</code>) and real time (<code>'RT'</code>) calculations should be done separately and sequentially for isolated systems (specified by <code>iperiodic = 0</code> in <code>&system</code>).
−	For periodic systems (specified by <code>iperiodic = 3</code> in <code>&system</code>), both ground state and real time calculations should be carried out as a single task (<code>calc_mode = 'GS_RT'</code>).
−
−	=== &control ===
−
−	Mandatory: none
−
−	&control
−	sysname = 'C2H2'
−	/
−
−	'C2H2' defined by <code>sysname = 'C2H2'</code> will be used in the filenames of output files.
−
−	=== &system ===
−
−	Mandatory: iperiodic, al, nstate, nelem, natom
−
−	&system
−	iperiodic = 0
−	al = 16d0, 16d0, 16d0
−	nstate = 5
−	nelem = 2
−	natom = 4
−	nelec = 10
−	/
−
−	<code>iperiodic = 0</code> indicates that the isolated boundary condition will be used in the calculation.
−	<code>al = 16d0, 16d0, 16d0</code> specifies the lengths of three sides of the rectangular parallelepiped where the grid points are prepared.
−	<code>nstate = 8</code> indicates the number of Kohn-Sham orbitals to be solved.
−	<code>nelec = 10</code> indicate the number of valence electrons in the system. Since the present code assumes that the system is spin saturated, <code>nstate</code> should be equal to or larger than <code>nelec/2</code>.
−	<code>nelem = 2</code> and <code>natom = 4</code> indicate the number of elements and the number of atoms in the system, respectively.
−
−	=== &pseudo ===
−
−	Mandatory: pseudo_file, izatom
−
−	&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.
−	<code>izatom(1) = 6</code> specifies the atomic number of the element 1.
−	<code>pseudo_file(1) = 'C_rps.dat'</code> indicates the filename of the pseudopotential of element 1.
−	<code>lmax_ps(1) = 1</code> and <code>lloc_ps(1) = 1</code> specify the maximum angular momentum of the pseudopotential projector and the angular momentum of the pseudopotential that will be treated as local, respectively.
−
−	=== &rgrid ===
−
−	Mandatory: dl or num_rgrid
−
−	&rgrid
−	dl = 0.25d0, 0.25d0, 0.25d0
−	/
−
−	<code>dl = 0.25d0, 0.25d0, 0.25d0</code> specifies the grid spacings in three Cartesian directions.
−	The grid spacing may also be specified by num_rgrid that specifies the number of grid points in three Cartesian directions.
−
−	=== &scf ===
−
−	Mandatory: nscf
−
−	&scf
−	ncg = 4
−	nscf = 1000
−	convergence = 'norm_rho_dng'
−	threshold_norm_rho = 1.d-15
−	/
−
−	<code>ncg</code> is the number of CG iterations in solving the Khon-Sham equation. <code>nscf</code> is the number of scf iterations. For isolated systems specified by <code>&system/iperiodic = 0</code>, the scf loop in the ground state calculation ends before the number of the scf iterations reaches <code>nscf</code>, if a convergence criterion is satisfied. There are several options for the convergence check. If the value of <code>norm_rho_dng</code> is specified, the convergence is examined by the squared difference of the electron density,
−
−	=== &atomic_coor ===
−
−	Mandatory: atomic_coor (it may be provided as a separate file)
−
−	&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.
−
−	== additional options ==
−
−
−	=== &parallel ===
−	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
−
−	&parallel
−	nproc_ob = 1
−	nproc_domain = 1,1,1
−	nproc_domain_s = 1,1,1
−	/
−
−	* <code>nproc_ob</code> specifies the number of MPI parallelization to divide the electron orbitals. The default value is 1 (no division).
−	* <code>nproc_domain(3)</code>specifies the number of MPI parallelization to divide the spatial grids of the electron orbitals in three Cartesian directions. The default values are (1/1/1) (no division).
−	* <code>nproc_domain_s(3)'</code> specifies the number of MPI parallelization to divide the spatial grids related to the electron density in three Cartesian directions.  The default values are (1/1/1) (no division).
−
−	The total number of processors must be equal to both <code>nproc_ob * nproc_domain(1) * nproc_domain(2) * nproc_domain(3)</code> and also <code>nproc_domain_s(1) * nproc_domain_s(2) * nproc_domain_s(3)</code>.  It should also be satisfied that <code>nproc_domain_s(1)</code> is a multiple of <code>nproc_domain(1)</code>, and the same relations to the second and third components.
−
−	=== &analysis ===
−	The following namelists specify whether the related output files are created or not after the calculation.
−
−	Mandatory: none
−
−	&analysis
−	out_psi = 'y'
−	out_dns = 'y'
−	out_dos = 'y'
−	out_pdos = 'y'
−	out_elf = 'y'
−	/
−
−	=== &units ===
−
−	Mandatory: none
−
−	&units
−	unit_system='A_eV_fs'
−	/
−
−	This namelist specifies the unit system to be used in the input file. If you do not specify it, atomic unit will be assumed.
−
−	For isolated systems (specified by <code>iperiodic = 0</code> in <code>&system</code>), the Angstrom/eV/fs are used for output files irrespective of the nameless value.
−
−	=== &calculation ===
−
−	Mandatory: calc_mode
−
−	&calculation
−	calc_mode = 'RT'
−	/
−
−	The value of the <code>calc_mode</code> should be one of <code>'GS'</code>, <code>'RT'</code>, and <code>'GS-RT'</code>. For the linear response calculation, we choose <code>'RT'</code>.
−	Note that the ground state (<code>'GS'</code>) and real time (<code>'RT'</code>) calculations should be done separately and sequentially for isolated systems (specified by <code>iperiodic = 0</code> in <code>&system</code>).
−	For periodic systems (specified by <code>iperiodic = 3</code> in <code>&system</code>), both ground state and real time calculations should be carried out as a single task (<code>calc_mode = 'GS_RT'</code>).
−
−	=== &control ===
−
−	Mandatory: none
−
−	&control
−	sysname = 'C2H2'
−	/
−
−	'C2H2' defined by <code>sysname = 'C2H2'</code> will be used in the filenames of output files.
−
−	=== &system ===
−
−	Mandatory: iperiodic, al, nstate, nelem, natom
−
−	&system
−	iperiodic = 0
−	al = 16d0, 16d0, 16d0
−	nstate = 5
−	nelem = 2
−	natom = 4
−	nelec = 10
−	/
−
−	These namelists and their values should be the same as those used in the ground state calculation.
−	See [[Explanations of input files (ground state of C2H2 molecule)-v.1.0.0#&system]].
−	<code>iperiodic = 0</code> indicates that isolated boundary condition is assumed.
−	<code>al = 16d0, 16d0, 16d0</code> specifies the lengths of three sides of a rectangular parallelepiped where the grid points are prepared.
−	<code>nstate = 8</code> indicates the number of Kohn-Sham orbitals to be solved.
−	<code>nelec = 10</code> indicate the number of valence electrons in the system.
−	<code>nelem = 2</code> and <code>natom = 4</code> indicate the number of elements and the number of atoms in the system, respectively.
−
−	=== &pseudo ===
−
−	Mandatory: pseudo_file, iZatom
−
−	&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
−	/
−
−	Information on pseudopotentials.
−	<code>izatom(1) = 6</code> indicates the atomic number of the element 1.
−	<code>pseudo_file(1) = 'C_rps.dat'</code> indicates the filename of the pseudopotential of element 1.
−	<code>lmax_ps(1) = 1</code> and <code>lloc_ps(1) = 1</code> indicate the maximum angular momentum of the pseudopotential projector and the angular momentum of the pseudopotential that will be treated as local, respectively.
−
−	=== &tgrid ===
−
−	Mandatory: dt, Nt
−
−	&tgrid
−	dt=1.25d-3
−	nt=5000
−	/
−
−	<code>dt=1.25d-3</code> specifies the time step of the time evolution calculations.
−	<code>nt=5000</code> specifies the number of time steps in the calculation.
−
−	=== &emfield ===
−
−	Mandatory: ae_shape1
−
−	&emfield
−	ae_shape1 = 'impulse'
−	epdir_re1 = 0.d0,0.d0,1.d0
−	/
−
−	This is a sample to calculate polarizability and oscillator distribution from real-time electron dynamics calculations.
−	Specifying <code>ae_shape1 = 'impulse'</code>, a weak impulsive force is applied to the isolated matter at ''t=0''
−	In output files, the polarizability and oscillator strength distribution, which is related to the imaginary part of the polarizability will be included.
−
−	=== &atomic_coor ===
−
−	Mandatory: none
−
−	&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
−	/
−
−	List of atomic coordinates. Last column corresponds to kinds of elements.
−
−	== additional options ==
−
−	=== &parallel ===
−
−	Mandatory: none
−
−	&parallel
−	nproc_ob = 1
−	nproc_domain = 1,1,1
−	nproc_domain_s = 1,1,1
−	/
−
−	Followings are explanation of each variable.
−	* <code>nproc_ob</code>: Number of MPI parallelization for orbitals that related to the wavefunction calculation.
−	* <code>nproc_domain(3)'</code>: Number of MPI parallelization for each direction in real-space that related to the wavefunction calculation.
−	* <code>nproc_domain_s(3)'</code>: Number of MPI parallelization for each direction in real-space that related to the electron density calculation.
−
−	Defaults are <code>0</code> for <code>nproc_ob</code>, <code>(0/0/0)</code> for <code>nproc_domain</code>, and <code>(0/0/0)</code> for <code>nproc_domain_s</code>. If users use the defauls, automatic proccess assignment is done. Users can also specify <code>nproc_ob</code>, <code>nproc_domain</code>, and <code>nproc_domain_s</code> manually. In that case, followings must be satisfied.
−	* nproc_ob</code> * <code>nproc_domain(1)</code> * <code>nproc_domain(2)</code>* <code>nproc_domain(3)</code>=total number of processors
−	* <code>nproc_domain_s(1)</code> * <code>nproc_domain_s(2)</code>* <code>nproc_domain_s(3)</code>=total number of processors
−	* <code>nproc_domain_s(1)</code> is a multiple of <code>nproc_domain(1)</code>
−	* <code>nproc_domain_s(2)</code> is a multiple of <code>nproc_domain(2)</code>
−	* <code>nproc_domain_s(3)</code> is a multiple of <code>nproc_domain(3)</code>
−
−	=== &analysis ===
−
−	Mandatory: none
−
−	&analysis
−	out_psi = 'y'
−	out_dns = 'y'
−	out_dos = 'y'
−	out_pdos = 'y'
−	out_elf = 'y'
−	/
−
−	These namelists specify the output files.
−	== Unit system ==
−
−	Hartree atomic units are used in this calculation by default.
−
−	== &calculation ==
−
−
−	&calculation
−	calc_mode = 'GS_RT'
−	/
−
−	The variable <code>calc_mode</code> is set to be <code>'GS_RT'</code> mode, which corresponds to execute the ground state (GS) and real-time (RT) calculation  with single calculation task.
−
−	== &control ==
−
−
−	&control
−	sysname = 'Si'
−	/
−
−	The variable <code>sysname</code> is set to be <code>'Si'</code>, which is used as the filename prefix of the outputs.
−
−
−
−	== &system ==
−
−
−
−	&system
−	iperiodic = 3
−	al = 10.26d0,10.26d0,10.26d0
−	isym = 8
−	crystal_structure = 'diamond'
−	nstate = 32
−	nelec = 32
−	nelem = 1
−	natom = 8
−	/
−
−	<code>iperiodic = 3</code> indicates that three dimensional periodic boundary condition (bulk crystal) is assumed.
−	<code>al = 10.26d0, 10.26d0, 10.26d0</code> specifies the lattice constans of the unit cell crystaline.
−	The variable <code>isym</code> indicates the symmetry in the unit cell.
−	Considering the bulk silicon crystal with the applied electric field parallel to the one lattice axis, <code>  isym = 8 </code> is preferred to speed up the calculation.
−	For more infomation, see [[Symmetry group of crystaline]].
−	<code>crystal_structure = 'diamond'</code> indicate the crystal structure of the considered material.
−	<code>nstate = 32</code> indicates the number of Kohn-Sham orbitals to be solved.
−	<code>nelec = 32</code> indicate the number of valence electrons in the system.
−	<code>nelem = 1</code> and <code>natom = 8</code> indicate the number of elements and the number of atoms in the system, respectively.
−
−	== &pseudo ==
−
−	&pseudo
−	iZatom(1)=14
−	pseudo_file(1) = './Si_rps.dat'
−	Lloc_ps(1)=2
−	/
−
−	<code>iZatom(1) = 14</code> indicates the atomic number of the element #1.
−	<code>pseudo_file(1) = 'Si_rps.dat'</code> indicates the  pseudopotential filename of element #1.
−	<code>Lloc_ps(1) = 2</code> indicate the angular momentum of the pseudopotential that will be treated as local.
−
−
−	== &functional ==
−
−	&functional
−	xc ='TBmBJ'
−	cval = 1d0
−	/
−
−	<code>xc ='TBmBJ'</code> specifies the type of exchange correlation potential. The TBmBJ indicates a meta-generalized gradient approximation proposed by Tran and Blaha [https://doi.org/10.1103/PhysRevLett.102.226401  Phys. Rev. Lett. 102, 226401 (2009)].
−	<code>cval</code> specifies the additional parameter of the TBmBJ potential. In the case of the silicon, <code>cval = 1d0</code> is prefered to reproduce the experimentally mesured optical constants.
−
−
−
−
−	== &rgrid ==
−
−	&rgrid
−	num_rgrid = 12,12,12
−	/
−
−	<code>num_rgrid=12,12,12</code> specifies number of the real space grids for single crystal calculation.
−
−
−	== &kgrid ==
−
−	&kgrid
−	num_kgrid = 4,4,4
−	/
−
−	<code>num_kgrid=4,4,4</code> specifies number of the k-space grids for single crystal calculation.
−
−
−	== &tgrid ==
−
−	&tgrid
−	nt=3000
−	dt=0.16
−	/
−
−	<code>dt=0.16</code> sets the time step of the time-evolution calculations.
−	<code>Nt=3000</code> indicates the number of the total time steps in the calculation.
−
−	== &propagation ==
−
−	&propagation
−	propagator='etrs'
−	/
−
−	<code>propagation</code> specifies the numerical method of the time evolution of the wave function. The <code>etrs</code> is Enforced time-reversal symmetry propagator.  [https://doi.org/10.1016/S0010-4655(02)00686-0 M.A.L. Marques, A. Castro, G.F. Bertsch, and A. Rubio, Comput. Phys. Commun., 151 60 (2003)].
−
−	== &scf ==
−
−	&scf
−	ncg = 5
−	nscf = 120
−	/
−
−	<code>ncg = 5</code> indicates the number of conjucate gradient step in the single scf calculation, and <code>nscf = 120</code> specifies the number of the SCF step.
−
−	== &emfield ==
−
−	&emfield
−	trans_longi = 'tr'
−	ae_shape1 = 'Acos2'
−	rlaser_int1 = 1d14
−	pulse_tw1 = 441.195136248d0
−	omega1 = 0.05696145187d0
−	epdir_re1 = 0.,0.,1.
−	/
−
−	<code>ae_shape1 = 'Acos2'</code> specifies the pulse shape of the electric field, having cos-square envelope.
−	<code>laser_int1</code> specifies maximum intensity of the applied electric field in unit of W/cm^2.
−	<code>epdir_re1 = 0.d0,0.d0,1.d0</code> identifies the unit vector of polarization direction.
−	Specifying the real part of the polarization vector by 'epdir_re1', linear polarization is assumed.
−	Using both the real ('epdir_re1') and imaginary ('epdir_im1') parts of the polarization vector, circularly (and general ellipsoidally) polarized pulses may also be described.
−
−	<code>omega1</code> specifies photon energy (frequency multiplied with plank constant).
−	<code>pulse_tw1</code> sets the pulse duration.
−	Note that it is not FWHM but a full duration of the sine-square envelope.
−	<code>phi_cep1</code> specifies the carrier envelope phase of the pulse.
−	It is possible to take two pulses simultaneously to simulate pump-probe experiments, adding information for two pulses.
−	The time delay can be indicated using the variable 't1_t2'.
−
−
−
−	== &atomic_coor ==
−
−	&atomic_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
−	/
−
−	List of atomic coordinates. Last column corresponds to kinds of elements.
−
−
−	== Unit system ==
−
−	Hartree atomic units are used in this calculation by default.
−
−	== &calculation ==
−
−
−	&calculation
−	calc_mode = 'GS_RT'
−	/
−
−	The variable <code>calc_mode</code> is set to be <code>'GS_RT'</code> mode, which corresponds to execute the ground state (GS) and real-time (RT) calculation  with single calculation task.s
−
−	== &control ==
−
−
−	&control
−	sysname = 'Si'
−	/
−
−	The variable <code>sysname</code> is set to be <code>'Si'</code>, which is used as the filename prefix of the outputs.
−
−
−
−	== &system ==
−
−
−
−	&system
−	iperiodic = 3
−	al = 10.26d0,10.26d0,10.26d0
−	isym = 8
−	crystal_structure = 'diamond'
−	nstate = 32
−	nelec = 32
−	nelem = 1
−	natom = 8
−	/
−
−	<code>iperiodic = 3</code> indicates that three dimensional periodic boundary condition (bulk crystal) is assumed.
−	<code>al = 10.26d0, 10.26d0, 10.26d0</code> specifies the lattice constans of the unit cell crystaline.
−	The variable <code>isym</code> indicates the symmetry in the unit cell.
−	Considering the bulk silicon crystal with the applied electric field parallel to the one lattice axis, <code>  isym = 8 </code> is preferred to speed up the calculation.
−	For more infomation, see [[Symmetry group of crystaline]].
−	<code>crystal_structure = 'diamond'</code> indicate the crystal structure of the considered material.
−	<code>nstate = 32</code> indicates the number of Kohn-Sham orbitals to be solved.
−	<code>nelec = 32</code> indicate the number of valence electrons in the system.
−	<code>nelem = 1</code> and <code>natom = 8</code> indicate the number of elements and the number of atoms in the system, respectively.
−
−	== &pseudo ==
−
−
−	&pseudo
−	iZatom(1)=14
−	pseudo_file(1) = './Si_rps.dat'
−	Lloc_ps(1)=2
−	/
−
−	<code>iZatom(1) = 14</code> indicates the atomic number of the element 1.
−	<code>pseudo_file(1) = 'Si_rps.dat'</code> indicates the filename of the pseudopotential of element 1.
−	<code>Lloc_ps(1) = 1</code> indicate the angular momentum of the pseudopotential that will be treated as local.
−
−
−	== &functional ==
−
−	&functional
−	xc ='TBmBJ'
−	cval = 1d0
−	/
−
−	<code>xc ='TBmBJ'</code> specifies the type of exchange correlation potential. The TBmBJ indicates a meta-generalized gradient approximation proposed by Tran and Blaha [https://doi.org/10.1103/PhysRevLett.102.226401  Phys. Rev. Lett. 102, 226401 (2009)].
−	<code>cval</code> specifies the additional parameter of the TBmBJ potential. In the case of the silicon, <code>cval = 1d0</code> is prefered to reproduce the experimentally mesured optical constants.
−
−
−	== Unit system ==
−
−	Hartree atomic units are employed in this calculation by default.
−
−	== &calculation ==
−
−
−	&calculation
−	calc_mode = 'GS_RT'
−	use_ms_maxwell = 'y'
−	/
−
−	The variable <code>calc_mode</code> is set to be <code>'GS_RT'</code> mode, which executes the ground state (GS) and real-time (RT) calculation  with single calculation task.
−	<pre>use_ms_maxwell='y'</pre> indicates the multiscale Maxwell-TDDFT calculation mode.
−
−	== &control ==
−
−	&control
−	sysname = 'Si'
−	/
−
−	The variable <code>sysname</code> is set to be <code>'Si'</code>, which is the filename prefix of the outputs.
−
−
−
−	== &system ==
−
−
−	&system
−	iperiodic = 3
−	al = 10.26d0,10.26d0,10.26d0
−	isym = 8
−	crystal_structure = 'diamond'
−	nstate = 32
−	nelec = 32
−	nelem = 1
−	natom = 8
−	/
−
−	<code>iperiodic = 3</code> indicates that three dimensional periodic boundary condition (bulk crystal) is supposed.
−	<code>al = 10.26d0, 10.26d0, 10.26d0</code> specifies the lattice constans of the unit cell crystaline.
−	The variable <code>isym</code> indicates the symmetry in the unit cell.
−	Considering the bulk silicon crystal with the applied electric field parallel to the one lattice axis, <code>  isym = 8 </code> is desirable to speed up the calculation.
−	For more information, see [[Symmetry group of crystalline]].
−	<code>crystal_structure = 'diamond'</code> indicate the crystal structure of the considered material.
−	<code>nstate = 32</code> indicates the number of Kohn-Sham orbitals in the computation.
−	<code>nelec = 32</code> is the number of valence electrons in the system.
−	<code>nelem = 1</code> and <code>natom = 8</code> is the number of elements and the number of atoms in the system, respectively.
−
−	== &pseudo ==
−
−
−	&pseudo
−	iZatom(1)=14
−	pseudo_file(1) = './Si_rps.dat'
−	Lloc_ps(1)=2
−	/
−
−	<code>iZatom(1) = 14</code> is  the number of atoms for the element 1.
−	<code>pseudo_file(1) = 'Si_rps.dat'</code> is the filename of the pseudopotential of element 1.
−	<code>Lloc_ps(1) = 1</code> indicate the angular momentum of the pseudopotential.
−
−	== &functional ==
−
−	&functional
−	xc ='PZ'
−	/
−
−	<code>xc ='PZ'</code> specifies the type of exchange correlation potential as LDA.
−
−
−
−
−	== &rgrid ==
−
−	&rgrid
−	num_rgrid = 12,12,12
−	/
−
−	<code>num_rgrid=12,12,12</code> specifies number of the real space grids for single crystal calculation.
−
−
−	== &kgrid ==
−
−	&kgrid
−	num_kgrid = 2,2,2
−	/
−
−	<code>num_kgrid=2,2,2</code> specifies number of the k-space grids for single crystal calculation.
−
−
−	== &tgrid ==
−
−	&tgrid
−	nt=4000
−	dt=0.08
−	/
−
−	<code>dt=0.16</code> sets the time step of the time-evolution calculations.
−	<code>Nt=3000</code> is the number of time steps in the calculation.
−
−	== &propagation ==
−
−	propagation
−	propagator='middlepoint'
−	/
−
−
−	<code>propagation='middlepoint'</code> specifies the numerical mathod of the time-evolution of the wave function.
−
−	== &scf ==
−
−	&scf
−	ncg = 5
−	nscf = 100
−	/
−
−	<code>ncg = 5</code> is the number of conjucate gradient step in the single scf calculation, and <code>nscf = 100</code> specifies the number of the SCF step.
−
−	== &emfield ==
−
−	&emfield
−	ae_shape1 = 'Acos2'
−	rlaser_int1 = 1d12
−	pulse_tw1 = 441.195136248d0
−	omega1 = 0.05696145187d0
−	epdir_re1 = 0.,0.,1.
−	/
−
−	<code>ae_shape1 = 'Acos2'</code> specifies the pulse shape of the electric field, having cos-square envelope.
−	<code>laser_int1</code> specifies maximum intensity of the applied electric field in unit of W/cm^2.
−	<code>epdir_re1 = 0,0,1</code> identifies the unit vector of polarization direction.
−	Specifying the real part of the polarization vector by 'epdir_re1', linear polarization is assumed.
−	Using both the real ('epdir_re1') and imaginary ('epdir_im1') parts of the polarization vector, circularly (and general ellipsoidally) polarized pulses may also be described.
−
−	<code>omega1</code> specifies photon energy (frequency multiplied with hbar).
−	<code>pulse_tw1</code> sets the pulse duration.
−	Note that it is not FWHM but a full duration of the sine-square envelope.
−	<code>phi_cep1</code> specifies the carrier envelope phase of the pulse.
−	It is possible to have two pulses simultaneously to simulate pump-probe experiments, adding information for two pulses.
−	The time delay can be indicated using the variable 't1_t2'.
−
−	== &multiscale ==
−
−	&multiscale
−	fdtddim = '1D'
−	twod_shape = 'periodic'
−	nx_m  = 4
−	ny_m  = 1
−	hX_m = 250d0
−	nksplit = 2
−	nxysplit = 1
−	nxvacl_m = -2000
−	nxvacr_m = 256
−	/
−
−	<code>fdtddim</code> specifies the dimension of the macro system. In the case of <code>fdtddim='1D'</code>, the one-dimensional light propagation in the slab region.
−	<code>twod_shape = 'periodic'</code> specifies the boundary condition of the EM field.
−	<code>nx_m, ny_m</code> is the number of the macroscopic grids for the x and y-direction, respectively.
−	<code>  nxvacl_m, nxvacr_m </code> indicates the number of the additional cells connected on the left-side and right-side of the material's surface.
−
−
−
−
−	== &atomic_coor ==
−
−	&atomic_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
−	/
−
−	List of atomic coordinates. Last column corresponds to kinds of elements.

---

Revision as of 09:34, 21 November 2017

Getting started

Welcome to SALMON Tutorial!

In this tutorial, we explain the use of SALMON from the very beginning, taking a few samples that cover applications of SALMON in several directions. We assume that you are in the computational environment of UNIX/Linux OS. First you need to download and install SALMON in your computational environment. If you have not yet done it, do it following the instruction, download-v.1.0.0 and Install and Run-v.1.0.0.

As described in Install and Run-v.1.0.0, you are required to prepare at least an input file and pseudopotential files to run SALMON. In the following, we present input files for several sample calculations and provide a brief explanation of the namelist variables that appear in the input files. You may modify the input files to execute for your own calculations. Pseudopotential files of elements that appear in the samples are also attached. We also present explanations of main output files.

We present 6 tutorials.

First 3 tutorials (Tutorial-1 ~ 3) are for an isolated molecule, acetylene C2H2. If you are interested in learning electron dynamics calculations in isolated systems, please look into these tutorials. In SALMON, we usually calculate the ground state solution first. This is illustrated in Tutorial-1. After finishing the ground state calculation, two tutorials of electron dynamics calculations are prepared. Tutorial-2 illustrates the calculation of linear optical responses in real time, obtaining polarizability and photoabsorption of the molecule. Tutorial-3 illustrates the calculation of electron dynamics in the molecule under a pulsed electric field.

Next 2 tutorials (Tutorial-4 ~ 5) are for a crystalline solid, silicon. If you are interested in learning electron dynamics calculations in extended periodic systems, please look into these tutorials. Since ground state calculations of small unit-cell systems are not computationally expensive and a time evolution calculation is usually much more time-consuming than the ground state calculation, we recommend to run the ground and the time evolution calculations as a single job. The following two tutorials are organized in that way. Tutorial-4 illustrates the calculation of linear response properties of crystalline silicon to obtain the dielectric function. Tutorial-5 illustrates the calculation of electron dynamics in the crystalline silicon induced by a pulsed electric field.

The final tutorial (Tutorial-6) is for an irradiation and a propagation of a pulsed light in a bulk silicon, coupling Maxwell equations for the electromagnetic fields of the pulsed light and the electron dynamics in the unit cells. This calculation is quite time-consuming and is recommended to execute using massively parallel supercomputers. Tutorial-6 illustrates the calculation of a pulsed, linearly polarized light irradiating normally on a surface of a bulk silicon.

C2H2 (isolated molecules)

Tutorial-1: Ground state of C2H2 molecule

In this tutorial, we learn the calculation of the ground state solution of acetylene (C2H2) molecule, solving the static Kohn-Sham equation. This tutorial will be useful to learn how to set up calculations in SALMON for any isolated systems such as molecules and nanoparticles. It should be noted that at present it is not possible to carry out the geometry optimization in SALMON. Therefore, atomic positions of the molecule are specified in the input file and are fixed during the calculations.

Input files

To run the code, following files are used:

file name	description
C2H2_gs.inp	input file that contains namelist variables and their values
C_rps.dat	pseodupotential file for carbon atom
H_rps.dat	pseudopotential file for hydrogen atom

• You may download the above 3 files (zipped file) from:

 Download zipped input and pseudopotential files

• In the input file C2H2_gs.inp, namelists variables are specified. Most of them are mandatory to execute the ground state calculation. We present their explanations below:

Explanations of input files (ground state of C2H2 molecule)-v.1.0.0

This will help you to prepare an input file for other systems that you want to calculate. A complete list of the namelist variables that can be used in the input file can be found in the downloaded file SALMON/manual/input_variables.md.

Output files

After the calculation, following output files are created in the directory that you run the code,

file name	description
C2H2_info.data	information on ground state solution
dns.cube	a cube file for electron density
elf.cube	electron localization function (ELF)
psi1.cube, psi2.cube, ...	electron orbitals
dos.data	density of states
pdos1.data, pdos2.data, ...	projected density of states
C2H2_gs.bin	binary output file to be used in the real-time calculation

• You may download the above files (zipped file, except for the binary file C2H2_gs.bin) from:

Download zipped output files

• Main results of the calculation such as orbital energies are included in C2H2_info.data. Explanations of the C2H2_info.data and other output files are described in:

Explanations of output files (ground state of C2H2 molecule)-v.1.0.0

Images

We show several image that are created from the output files.

image	files used to create the image
highest occupied molecular orbital (HOMO)	psi1.cube, psi2.cube, ...
electron density	dns.cube
electron localization function	elf.cube

Tutorial-2: Polarizability and photoabsorption of C2H2 molecule

In this tutorial, we learn the linear response calculation in the acetylene (C2H2) molecule, solving the time-dependent Kohn-Sham equation. The linear response calculation provides the polarizability and the oscillator strength distribution of the molecule. This tutorial should be carried out after finishing the ground state calculation that was explained in Tutorial-1. In the calculation, an impulsive perturbation is applied to all electrons in the C2H2 molecule along the molecular axis which we take z axis. Then a time evolution calculation is carried out without any external fields. During the calculation, the electric dipole moment is monitored. After the time evolution calculation, a time-frequency Fourier transformation is carried out for the electric dipole moment to obtain the frequency-dependent polarizability. The imaginary part of the frequency-dependent polarizability is proportional to the oscillator strength distribution and the photoabsorption cross section.

Input files

To run the code, the input file C2H2_rt_response.inp that contains namelist variables and their values for the linear response calculation is required. The binary file C2H2_gs.bin that is created in the ground state calculation and pseudopotential files are also required. The pseudopotential files should be the same as those used in the ground state calculation.

file name	description
C2H2_rt_response.inp	input file that contains namelist variables and their values
C_rps.dat	pseodupotential file for carbon
H_rps.dat	pseudopotential file for hydrogen
C2H2_gs.bin	binary file created in the ground state calculation

• You may download the C2H2_rt_response.inp file (zipped file) from:

 Download zipped input file

• In the input file C2H2_rt_response.inp, namelists variables are specified. Most of them are mandatory to execute the linear response calculation. We present their explanations below:

Explanations of input files (polarizability and photoabsorption of C2H2 molecule)-v.1.0.0

This will help you to prepare the input file for other systems that you want to calculate. A complete list of the namelist variables that can be used in the input file can be found in the downloaded file SALMON/manual/input_variables.md.

Output files

After the calculation, following output files are created in the directory that you run the code,

file name	description
C2H2_lr.data	polarizability and oscillator strength distribution as functions of energy
C2H2_p.data	components of dipole moment as functions of time

• You may download the above files (zipped file) from:

Download zipped output files

• Explanations of the output files are given in:

Explanations of output files (polarizability and photoabsorption of C2H2 molecule)-v.1.0.0

Tutorial-3: Electron dynamics in C2H2 molecule under a pulsed electric field

In this tutorial, we learn the calculation of the electron dynamics in the acetylene (C2H2) molecule under a pulsed electric field, solving the time-dependent Kohn-Sham equation. As outputs of the calculation, such quantities as the total energy and the electric dipole moment of the system as functions of time are calculated. This tutorial should be carried out after finishing the ground state calculation that was explained in Tutorial-1. In the calculation, a pulsed electric field that has cos^2 envelope shape is applied. The parameters that characterize the pulsed field such as magnitude, frequency, polarization direction, and carrier envelope phase are specified in the input file.

Input files

To run the code, following files are used. The C2H2.data file is created in the ground state calculation. Pseudopotential files are already used in the ground state calculation. Therefore, C2H2_rt_pulse.inp that specifies namelist variables and their values for the pulsed electric field calculation is the only file that the users need to prepare.

file name	description
C2H2_rt_pulse.inp	input file that contain namelist variables and their values.
C_rps.dat	pseodupotential file for Carbon
H_rps.dat	pseudopotential file for Hydrogen
C2H2.data	binary file created in the ground state calculation

• You may download the C2H2_rt_pulse.inp file (zipped file) from:

 Download zipped input file

• In the input file C2H2_rt_pulse.inp, namelists variables are specified. Most of them are mandatory to execute the calculation of electron dynamics induced by a pulsed electric field. We present explanations of the namelist variables that appear in the input file in:

Explanations of input files (C2H2 molecule under a pulsed electric field)-v.1.0.0

This will help you to prepare the input file for other systems and other pulsed electric fields that you want to calculate. A complete list of the namelist variables that can be used in input files can be found at ???.

Output files

After the calculation, following output files are created in the directory that you run the code,

file name	description
C2H2_p.data	components of the electric dipole moment as functions of time
C2H2_ps.data	power spectrum that is obtained by a time-frequency Fourier transformation of the electric dipole moment

• You may download the above files (zipped file) from:

Download zipped output files

• Explanations of the files are described in:

Explanations of input files (C2H2 molecule under a pulsed electric field)-v.1.0.0

Crystalline silicon (periodic solids)

Tutorial-4: Dielectric function of crystalline silicon

In this tutorial, we learn the linear response calculation of the crystalline silicon of a diamond structure. Calculation is done in a cubic unit cell that contains eight silicon atoms. Since the ground state calculation costs much less computational time than the time evolution calculation, both calculations are successively executed. After finishing the ground state calculation, an impulsive perturbation is applied to all electrons in the unit cell along z direction. Since the dielectric function is isotropic in the diamond structure, calculated dielectric function should not depend on the direction of the perturbation. During the time evolution, electric current averaged over the unit cell volume is calculated. A time-frequency Fourier transformation of the electric current gives us a frequency-dependent conductivity. The dielectric function may be obtained from the conductivity using a standard relation.

Input files

To run the code, following files are used:

file name	description
Si_gs_rt_response.inp	input file that contain namelist variables and their values.
Si_rps.dat	pseodupotential file of silicon

• You may download the above 2 files (zipped file) from:

 Download zipped input and pseudopotential files

• In the input file Si_gs_rt_response.inp, namelists variables are specified. Most of them are mandatory to execute the calculation. We present explanations of the namelist variables that appear in the input file in:

Explanations of input files (dielectric function of crystalline silicon)-v.1.0.0

This will help you to prepare the input file for other systems that you want to calculate. A complete list of the namelist variables that can be used in input files can be found at ???.

Output files

After the calculation, following output files are created in the directory that you run the code,

file name	description
Si_eigen.data	energy eigenvalues of orbitals
Si_gs_info.data	information of ground state calculation
Si_k.data	information on k-points
Si_rt.data	electric field, vector potential, and current as functions of time
Si_lr.data	Fourier spectra of the dielectric functions

• You may download the above files (zipped file) from:

Download zipped output files

• Explanations of the output files are described in:

Explanation of output fiels (dielectric function of crystalline silicon)-v.1.0.0

Tutorial-5: Electron dynamics in crystalline silicon under a pulsed electric field

In this tutorial, we learn the calculation of electron dynamics in a unit cell of crystalline silicon of a diamond structure. Calculation is done in a cubic unit cell that contains eight silicon atoms. Since the ground state calculation costs much less computational time than the time evolution calculation, both calculations are successively executed. After finishing the ground state calculation, a pulsed electric field that has cos^2 envelope shape is applied. The parameters that characterize the pulsed field such as magnitude, frequency, polarization, and carrier envelope phase are specified in the input file.

Input files

To run the code, following files are used:

file name	description
Si_gs_rt_pulse.inp	input file that contain namelist variables and their values.
Si_rps.dat	pseodupotential file for Carbon

• You may download the above 2 files (zipped file) from:

 Download zipped input and pseudopotential files

• In the input file Si_gs_rt_pulse.inp, namelists variables are specified. Most of them are mandatory to execute the calculation. We present explanations of the namelist variables that appear in the input file in:

Explanation of input files (crystalline silicon under a pulsed electric field)-v.1.0.0

This will help you to prepare the input file for other systems that you want to calculate. A complete list of the namelist variables that can be used in input files can be found at ???.

Output files

After the calculation, following output files are created in the directory that you run the code,

file name	description
Si_eigen.data	energy eigenvalues of orbitals
Si_k.data	information on k-points
Si_gs_info.data	information on the ground state
Si_rt.data	electric field, vector potential, and current as functions of time

• You may download the above files (zipped file) from:

Download zipped output files

• Explanations of the output files are described in:

Explanation of output files (crystalline silicon under a pulsed electric field)-v.1.0.0

Maxwell + TDDFT multiscale simulation

Tutorial-6: Pulsed-light propagation through a silicon thin film

In this tutorial, we learn the calculation of the propagation of a pulsed light through a thin film of crystalline silicon. We consider a silicon thin film of ?? nm thickness, and an irradiation of a few-cycle, linearly polarized pulsed light normally on the thin film. First, to set up initial orbitals, the ground state calculation is carried out. The pulsed light locates in the vacuum region in front of the thin film. The parameters that characterize the pulsed light such as magnitude and frequency are specified in the input file. The calculation ends when the reflected and transmitted pulses reach the vacuum region.

Input files

To run the code, following files are used:

file name	description
Si_gs_rt_multiscale.inp	input file that contain namelist variables and their values.
Si_rps.dat	pseodupotential file for silicon

• You may download the above two files (zipped file) from:

 Download zipped input and pseudopotential files

• In the input file Si_gs_rt_multiscale.inp, namelists variables are specified. Most of them are mandatory to execute the calculation. We present explanations of the namelist variables that appear in the input file in:

Explanation of input files (pulsed-light propagation through a silicon thin film)-v.1.0.0

This will help you to prepare the input file for other systems that you want to calculate. A complete list of the namelist variables that can be used in input files can be found at ???.

Output files

After the calculation, following output files are created in the directory that you run the code,

file name	description
Si_Ac_xxxxxx.out	EM field and electron energy distribution at the macroscpic grid
Si_Ac_M_xxxxxx.out	Vector potential field and current density at individual macropoints
Si_Ac_vac.out

• You may download the above files (zipped file) from:

Download zipped output files

• Explanations of the output files are described in:

Explanation of output files (pulsed-light propagation through a silicon thin film)-v.1.0.0

Namelists and their values

We here summarize namelists that appear in this Tutorial.