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提供: ComplexRI: Manual
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==Manual==


{|class="wikitable"
{|class="wikitable"
! Index
! Input of ComplexRI
|-
|-
|[[#Overview|Overview]]
|[[Input#Information of ATR-IR experiment|Information of ATR-IR experiment]]
|-
|-
|[[#Developing History|Developing History]]
|[[Input#Control parameters of ComplexRI fitting|Control parameters of ComplexRI fitting]]
|-
|[[#Tutorial|Tutorial]]
|-
|[[#Manual|Manual]]
|-
|[[#Theory|Theory]]
|-
|[[#FAQ|FAQ]]
|}
|}


== Overview ==
The complex refractive index is a basic property in the study of light-matter interactions and spectroscopy. Especially in the sum frequency generation (SFG) vibrational spectroscopy studies, the analysis of SFG spectra requires detailed information of the Fresnel factors in the typical three-layer interface model. The dispersion of Fresnel factors in SFG spectra originates from the complex refractive index of the liquid. Studies <ref name = "ref1" /> have shown that the dispersion of the Fresnel factor may become significant and seriously change the analysis results of SFG spectra. However, the complex refractive index in the Infrared region is somehow unavailable for most commonly used liquids in SFG studies. Therefore, we have developed ComplexRI software package to obtain the complex refractive index of any liquids by using the ATR-IR spectra. The output of ComplexRI is the complex refractive index in IR region. Users can specify the target vibrational regions, such as vibrational modes of different functional groups.
==Developing History==
The development was done in the lab of computational molecular science at Tohoku University.
The main code was first developed by Wang in 2019 when he investigated the dispersion of Fresnel factor in electrode/electrolyte interfaces. <ref name = "ref1" /> In 2020, Murata further extended the code and generated a complex refractive index database with about 20 commonly used liquids in SFG studies. <ref name = "ref2" /> Wang used the database and discussed the general influence of dispersion of Fresnel factor in the SFG spectra analysis. <ref name = "ref3" />. In 2021, the program code was summarized and opened to the website by Kamimura under the supervise of Wang and Morita. The automatic fitting procedure is updated. Kamimura and Wang also created the MediaWiki manual page for ComplexRI.
Many thanks to the experimental collaborators during the development.
: Dr. Satoshi Nihonyanagi (RIKEN), Dr. Ken-ichi Inoue (Tohoku Univ.), Prof. Shen Ye (Tohoku Univ.), Dr. Tahei Tahara  (RIKEN).
== Tutorial ==
{|class="wikitable"
{|class="wikitable"
! Examples to use ComplexRI
! Output of ComplexRI
|-
|-
|[[Tutorial01|Tutorial01]]： Automatic Mode
|[[Output#Stardard output of ComplexRI|Stardard output of ComplexRI]]
|-
|-
|[[Tutorial02|Tutorial02]]： Manual Mode
|[[Output#Download your results|Download your results]]
|}
|}


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==Manual==
== Tutorial ==
 
{|class="wikitable"
{|class="wikitable"
! Input of ComplexRI
! Examples to use ComplexRI
|-
|[[Input#Information of ATR-IR experiment|Information of ATR-IR experiment]]
|-
|[[Input#Control parameters of ComplexRI fitting|Control parameters of ComplexRI fitting]]
|}
 
{|class="wikitable"
! Output of ComplexRI
|-
|-
|[[Output#Stardard output of ComplexRI|Stardard output of ComplexRI]]
| Tutorial01：[[Tutorial01| Automatic Mode]]
|-
|-
|[[Output#Download your results|Download your results]]
| Tutorial02： [[Tutorial02|Manual Mode]]
|}
|}


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|[[Theory#ATR-IR data|Calculated reflectance of ATR-IR from complex refractive index]]
|[[Theory#ATR-IR data|Calculated reflectance of ATR-IR from complex refractive index]]
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|[[Theory#Fitting procedure|Fitting procedure]]： How to Fit the ATR-IR spectra
|[[Theory#Fitting procedure| How to Fit the ATR-IR spectra]]
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|[[Theory#Auto Fitting|Auto Fitting]]： Automatically determine the initial parameters in fitting procedure
|[[Theory#Auto Fitting|Automatically determine the initial parameters in fitting procedure]]
|}
|}


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==FAQ==
<div style="font-size: 150%;"> 1. How to cite ComplexRI </div>
: If you found Complex is helpful, please cite the following references.
<references>
<ref name = "ref1">"Effect of Frequency-Dependent Fresnel Factor on the Vibrational Sum Frequency Generation Spectra for Liquid/Solid Interfaces"
Lin Wang, Satoshi Nihonyanagi, Ken-ichi Inoue, Kei Nishikawa, Akihiro Morita, Shen Ye, Tahei Tahara, J. Phys. Chem. C, 123(25) 15665-15673 (2019).</ref>
<ref name = "ref2">"Dispersion of Complex Refractive Indices for Intense Vibrational Bands. I Quantitative Spectra"
Ryo Murata, Ken-ichi Inoue, Lin Wang, Shen Ye, and Akihiro Morita, J. Phys. Chem. B, 125(34), 9794-9803 (2021).</ref>
<ref name = "ref3">"Dispersion of Complex Refractive Indices for Intense Vibrational Bands. II Implication to Sum Frequency Generation Spectroscopy"
Lin Wang, Ryo Murata, Ken-ichi Inoue, Shen Ye, and Akihiro Morita, J. Phys. Chem. B, 125(34), 9804-9810 (2021).</ref>
</references>


[http://comp.chem.tohoku.ac.jp/mediawiki/index.php/en/ComplexRI Top of this page]
[http://comp.chem.tohoku.ac.jp/mediawiki/index.php/en/ComplexRI Top of this page]

2022年2月14日 (月) 01:54時点における最新版

Manual

Input of ComplexRI
Information of ATR-IR experiment
Control parameters of ComplexRI fitting
Output of ComplexRI
Stardard output of ComplexRI
Download your results

Tutorial

Examples to use ComplexRI
Tutorial01： Automatic Mode
Tutorial02： Manual Mode

Theory

Calculated reflectance of ATR-IR from complex refractive index
How to Fit the ATR-IR spectra
Automatically determine the initial parameters in fitting procedure

Top of this page

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