Tutorial-v.1.0.0

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 contain namelist variables and their values.
C_rps.dat	pseodupotential file for Carbon
H_rps.dat	pseudopotential file for Hydrogen

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

 Download zipped input and pseudopotential files

• You can view the input file C2H2_gs.inp in:

View C2H2_gs.inp file

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

Explanation of C2H2_gs.inp file

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 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-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

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

Download zipped output files

• Main results of the calculation such as orbital energies are included in C2H2.info. You can see the file:

See C2H2.info file

• Explanations of the C2H2.info and other output files are described in:

Explanation of C2H2-info.data and other output files

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, following files are used. The ??? file is created in the ground state calculation. Pseudopotential files are already used in the ground state calculation. Therefore, C2H2_rt_response.inp that specifies namelist variables and their values for the linear response calculation is the only file that the users need to prepare.

file name	description
C2H2_rt_response.inp	input file that contain namelist variables and their values.
C_rps.dat	pseodupotential file for Carbon
H_rps.dat	pseudopotential file for Hydrogen
???	binary file created in the ground state calculation

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

 Download zipped input file

• You can view the input file C2H2_rt_response.inp in:

View C2H2_rt_response.inp 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 explanations of the namelist variables that appear in the input file in:

Explanation of C2H2_rt_response.inp file

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
C2H2-RT.data	components of the electric dipole moment as functions of time
C2H2-ALP.data	polarizability and oscillator strength distribution as functions of energy

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

Download zipped output files

• Explanations of the output files, C2H2-RT.data and C2H2-ALP.data, are given in:

Explanation of C2H2-RT.data and C2H2-ALP.data

Tutorial-3: Electron dynamics of 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 ??? 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
???	binary file created in the ground state calculation

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

 Download zipped input file

• You can view the input file C2H2_rt_pulse.inp in:

View C2H2_rt_pulse.inp 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:

Explanation of C2H2_rt_pulse.inp file

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-RT.data	components of the electric dipole moment as functions of time
C2H2-ALP.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:

Explanation of C2H2-RT.data and C2H2-ALP.data

Crystalline silicon (periodic solids)

Tutorial-1: Ground state and dielectric function of crystalline silicon

In this tutorial, we learn the calculation of the ground state solution of acetylene Si bulk crystaline, solving the time-dependent Kohn-Sham (TDKS) equation.

Input files

To run the code, following files are used:

file name	description
input_lr_Si.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

• You can view the input file C2H2_gs.inp in:

View input_lr_Si.inp file

• In the input file input_lr_Si.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_lr_Si.inp file

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	information on ground state solution
Si_rt.data	electron localization function (ELF)

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

Download zipped output files

Tutorial-2: Ground state and electron dynamics in crystalline silicon under a pulsed electric field

In this tutorial, we learn the calculation of the temporal response of Si bulk crystaline under the intense light-pulse irradiation.

Input files

To run the code, following files are used:

file name	description
input_sc_Si.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

• You can view the input file input_sc_Si.inp in:

View input_sc_Si.inp file

• In the input file input_sc_Si.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 for Si response input files 

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	information on ground state solution
Si_rt.data	electron localization function (ELF)

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

Download zipped output files

Light propagation in bulk silicon (Maxwell + TDDFT)

Tutorial-1: Light propagation in thin film bulk silicon

In this tutorial, we learn the calculation of the light propagation problem in the thin film silicon crystalline.

Input files

To run the code, following files are used:

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

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

 Download zipped input and pseudopotential files

• You can view the input file input_ms_Si.inp in:

View input_ms_Si.inp file

• In the input file input_ms_Si.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 for Si response input files 

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_??????.out	EM field and electron energy distribution at the macroscpic grid
Si_Ac_M_??????.out	Vector potential field and current density at individual macropoints

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

Download zipped output files