Difference between revisions of "エクササイス"

Revision as of 20:26, 20 January 2018

はじめに

SALMONエクササイスへようこそ！

このエクササイスでは、SALMONの多岐にわたる応用をカバーする いくつかのサンプルを用いて、基本からSALMONの使い方を説明します。 以下では、UNIX/Linux OSの計算環境にあることを前提にします。 最初に、あなたの計算環境にSALMONをダウンロードしインストールすることが必要です。 まだ行っていない場合は、ダウンロードとインストールと実行に従い作業してください。

インストールと実行で述べたように、SALMONを実行するためには少なくとも 入力ファイルと擬ポテンシャルファイルが必要です。 以下では、いくつかのサンプル計算に対する入力ファイルを示し、その入力ファイルに 現れるネームリスト変数の簡単な説明を行います。 その入力ファイルを修正して、あなた自身が行いたい計算を実行することができるでしょう。 サンプルに含まれている元素の擬ポテンシャルも提供されています。 主要な出力ファイルの説明も行います。

以下では６つのエクササイスを紹介します。

最初の３つのエクササイス（エクササイス-1~3）は、孤立したアセチレン分子C2H2に対するものです。 もし孤立した系の電子ダイナミクス計算に興味がある場合は、これらのエクササイスをごらんください。 SALMONでは、通常最初に基底状態計算を行います。 これは、エクササイス-1で説明します。 基底状態計算が終わったのち、２つの電子ダイナミクス計算が用意されています。 エクササイス-2では、分子の分極率と光吸収を得る 実時間での線形光応答計算を示します。 エクササイス-3では、 パルス電場中にある分子の電子ダイナミクス計算を示します。

次の２つのエクササイス(エクササイス-4~5)は、結晶固体シリコンに対するものです。 もし無限周期系における電子ダイナミクス計算を学ぶことに興味があれば、これらのエクササイスを見てください。 小さな単位セルを持つ系の基底状態計算は容易であり、時間発展計算の方がはるかに計算時間がかかるため、 基底状態と時間発展の計算を一つのジョブとして実行することを推奨します。 以下の２つのエクササイスも、そのようになっています。 エクササイス-4では、結晶シリコンの誘電関数を得るための 線形応答性質の計算を示します。 エクササイス5 では、パルス電場により結晶シリコンに誘起される電子ダイナミクス計算を示します。

最後のエクササイス(エクササイス-6)は、バルクシリコンにおけるパルス光の入射と伝播に対して、 パルス光の電磁場に対するマクスウェル方程式と単位セルの電子ダイナミクス計算を結合したものです。 ものです。 これは大きな計算時間を必要とするため、大規模並列スパコンの利用が推奨されます。 エクササイス-6で、 バルクシリコンの表面に垂直に入射する直線偏光パルス光の入射計算を示します。

C2H2 (孤立分子)

エクササイス-1: C2H2分子の基底状態

このエクササイスでは、静的コーン・シャム方程式を解くことにより、アセチレン分子(C2H2)の基底状態計算を学びます。 このエクササイスは、分子やナノ粒子のような孤立した系に対して、SALMONを用いた計算を行う準備をどのように すれば良いかを知るのに有用です。今のところ、SALMONで構造最適化を実行することはできないことに注意して ください。分子の原子位置は入力ファイルて指定され、計算の過程では固定されます。

入力ファイル

コードを実行するために、以下のファイルが必要です。

• 上記の３つのファイル（圧縮ファイル）は、以下からダウンロードできます:

 圧縮された入力ファイルと擬ポテンシャルファイルをダウンロード

• 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)

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,

• 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)

Images

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

Exercise-2: Polarizability and photoabsorption of C2H2 molecule

In this exercise, 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 exercise should be carried out after finishing the ground state calculation that was explained in Exercise-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.

• 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)

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,

• 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)

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

In this exercise, 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 Exercise-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.

• 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)

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 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,

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

Download zipped output files

• Explanations of the files are described in:

Explanations of output files (C2H2 molecule under a pulsed electric field)

Crystalline silicon (periodic solids)

Exercise-4: Dielectric function of crystalline silicon

In this exercise, 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:

• 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)

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,

• 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)

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

In this exercise, 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:

• 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)

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,

• 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)

Maxwell + TDDFT multiscale simulation

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

In this exercise, 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:

• 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)

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,

• 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)